Search results for the GEO ID: GSE37573  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM922021 | GPL201 |
|
1_100688_0hr_Serum
|
ebvBcells from Norm donor1 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 0hr_serum control
|
| Sample_geo_accession | GSM922021
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922021/suppl/GSM922021_1_100688_0hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922022 | GPL201 |
|
2_100688_1hr_Serum
|
ebvBcells from Norm donor1 1hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 1hr_serum control
|
| Sample_geo_accession | GSM922022
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922022/suppl/GSM922022_2_100688_1hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922023 | GPL201 |
|
3_100688_0.5hr_Serum
|
ebvBcells from Norm donor1 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 .5hr_serum control
|
| Sample_geo_accession | GSM922023
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922023/suppl/GSM922023_3_100688_.5hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922024 | GPL201 |
|
4_100688_2hr_Serum
|
ebvBcells from Norm donor1 2hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 2hr_serum control
|
| Sample_geo_accession | GSM922024
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922024/suppl/GSM922024_4_100688_2hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922025 | GPL201 |
|
5_100688_4hr_Serum
|
ebvBcells from Norm donor1 4hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 4hr_serum control
|
| Sample_geo_accession | GSM922025
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922025/suppl/GSM922025_5_100688_4hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922026 | GPL201 |
|
6_100688_8hr_Serum
|
ebvBcells from Norm donor1 8hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 8hr_serum control
|
| Sample_geo_accession | GSM922026
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922026/suppl/GSM922026_6_100688_8hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922027 | GPL201 |
|
7_100688_16hr_Serum
|
ebvBcells from Norm donor1 16hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 16hr_serum control
|
| Sample_geo_accession | GSM922027
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922027/suppl/GSM922027_7_100688_16hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922028 | GPL201 |
|
8_100688_24hr_Serum
|
ebvBcells from Norm donor1 24hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 24hr_serum control
|
| Sample_geo_accession | GSM922028
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922028/suppl/GSM922028_8_100688_24hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922029 | GPL201 |
|
9_316_0hr_Serum
|
ebvBcells from Norm donor2 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 0hr_serum control
|
| Sample_geo_accession | GSM922029
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922029/suppl/GSM922029_9_316_0hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922030 | GPL201 |
|
10_316_0.5hr_Serum
|
ebvBcells from Norm donor2 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 .5hr_serum control
|
| Sample_geo_accession | GSM922030
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922030/suppl/GSM922030_10_316_0.5hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922031 | GPL201 |
|
11_316_1hr_Serum
|
ebvBcells from Norm donor2 1hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 1hr_serum control
|
| Sample_geo_accession | GSM922031
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922031/suppl/GSM922031_11_316_1hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922032 | GPL201 |
|
12_316_2hr_Serum
|
ebvBcells from Norm donor2 2hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 2hr_serum control
|
| Sample_geo_accession | GSM922032
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922032/suppl/GSM922032_12_316_2hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922033 | GPL201 |
|
13_316_4hr_Serum
|
ebvBcells from Norm donor2 4hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 4hr_serum control
|
| Sample_geo_accession | GSM922033
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922033/suppl/GSM922033_13_316_4hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922034 | GPL201 |
|
14_316_8hr_Serum
|
ebvBcells from Norm donor2 8hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 8hr_serum control
|
| Sample_geo_accession | GSM922034
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922034/suppl/GSM922034_14_316_8hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922035 | GPL201 |
|
15_316_16hr_Serum
|
ebvBcells from Norm donor2 16hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 16hr_serum control
|
| Sample_geo_accession | GSM922035
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922035/suppl/GSM922035_15_316_16hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922036 | GPL201 |
|
16_316_24hr_Serum
|
ebvBcells from Norm donor2 24hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 24hr_serum control
|
| Sample_geo_accession | GSM922036
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922036/suppl/GSM922036_16_316_24hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922037 | GPL201 |
|
49_101884_0hr_Serum
|
ebvBcells from Norm donor1 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 0hr_serum control
|
| Sample_geo_accession | GSM922037
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922037/suppl/GSM922037_49_101884_0hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922038 | GPL201 |
|
50_101884_0.5hr_Serum
|
ebvBcells from Norm donor1 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 .5hr_serum control
|
| Sample_geo_accession | GSM922038
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922038/suppl/GSM922038_50_101884_0.5hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922039 | GPL201 |
|
51_101884_1hr_Serum
|
ebvBcells from Norm donor1 1hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 1hr_serum control
|
| Sample_geo_accession | GSM922039
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922039/suppl/GSM922039_51_101884_1hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922040 | GPL201 |
|
52_101884_2hr_Serum
|
ebvBcells from Norm donor1 2hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 2hr_serum control
|
| Sample_geo_accession | GSM922040
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922040/suppl/GSM922040_52_101884_2hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922041 | GPL201 |
|
53_101884_4hr_Serum
|
ebvBcells from Norm donor1 4hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 4hr_serum control
|
| Sample_geo_accession | GSM922041
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922041/suppl/GSM922041_53_101884_4hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922042 | GPL201 |
|
54_101884_8hr_Serum
|
ebvBcells from Norm donor1 8hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 8hr_serum control
|
| Sample_geo_accession | GSM922042
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922042/suppl/GSM922042_54_101884_8hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922043 | GPL201 |
|
55_101884_16hr_Serum
|
ebvBcells from Norm donor1 16hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 16hr_serum control
|
| Sample_geo_accession | GSM922043
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922043/suppl/GSM922043_55_101884_16hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922044 | GPL201 |
|
56_101884_24hr_Serum
|
ebvBcells from Norm donor1 24hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor1 24hr_serum control
|
| Sample_geo_accession | GSM922044
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922044/suppl/GSM922044_56_101884_24hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922045 | GPL201 |
|
57_301948_0hr_Serum
|
ebvBcells from Norm donor2 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 0hr_serum control
|
| Sample_geo_accession | GSM922045
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922045/suppl/GSM922045_57_301948_0hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922046 | GPL201 |
|
58_301948_0.5hr_Serum
|
ebvBcells from Norm donor2 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 .5hr_serum control
|
| Sample_geo_accession | GSM922046
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922046/suppl/GSM922046_58_301948_0.5hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922047 | GPL201 |
|
59_301948_1hr_Serum
|
ebvBcells from Norm donor2 1hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 1hr_serum control
|
| Sample_geo_accession | GSM922047
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922047/suppl/GSM922047_59_301948_1hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922048 | GPL201 |
|
60_301948_2hr_Serum
|
ebvBcells from Norm donor2 2hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 2hr_serum control
|
| Sample_geo_accession | GSM922048
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922048/suppl/GSM922048_60_301948_2hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922049 | GPL201 |
|
61_301948_4hr_Serum
|
ebvBcells from Norm donor2 4hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 4hr_serum control
|
| Sample_geo_accession | GSM922049
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922049/suppl/GSM922049_61_301948_4hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922050 | GPL201 |
|
62_301948_8hr_Serum
|
ebvBcells from Norm donor2 8hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 8hr_serum control
|
| Sample_geo_accession | GSM922050
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922050/suppl/GSM922050_62_301948_8hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922051 | GPL201 |
|
63_301948_16hr_Serum
|
ebvBcells from Norm donor2 16hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 16hr_serum control
|
| Sample_geo_accession | GSM922051
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922051/suppl/GSM922051_63_301948_16hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922052 | GPL201 |
|
64_301948_24hr_Serum
|
ebvBcells from Norm donor2 24hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Norm donor2 24hr_serum control
|
| Sample_geo_accession | GSM922052
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922052/suppl/GSM922052_64_301948_24hr_Serum.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922053 | GPL201 |
|
65_316_0hr_BCRFCR
|
ebvBcells from Lupus patient1 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 0hr_BCRFCR
|
| Sample_geo_accession | GSM922053
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922053/suppl/GSM922053_65_316_0hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922054 | GPL201 |
|
66_316_0.5hr_BCRFCR
|
ebvBcells from Lupus patient1 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922054
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922054/suppl/GSM922054_66_316_0.5hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922055 | GPL201 |
|
67_316_1hr_BCRFCR
|
ebvBcells from Lupus patient1 1hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 1hr_BCRFCR
|
| Sample_geo_accession | GSM922055
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922055/suppl/GSM922055_67_316_1hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922056 | GPL201 |
|
68_316_2hr_BCRFCR
|
ebvBcells from Lupus patient1 2hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 2hr_BCRFCR
|
| Sample_geo_accession | GSM922056
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922056/suppl/GSM922056_68_316_2hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922057 | GPL201 |
|
69_316_4hr_BCRFCR
|
ebvBcells from Lupus patient1 4hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 4hr_BCRFCR
|
| Sample_geo_accession | GSM922057
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922057/suppl/GSM922057_69_316_4hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922058 | GPL201 |
|
70_316_8hr_BCRFCR
|
ebvBcells from Lupus patient1 8hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 8hr_BCRFCR
|
| Sample_geo_accession | GSM922058
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922058/suppl/GSM922058_70_316_8hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922059 | GPL201 |
|
71_316_16hr_BCRFCR
|
ebvBcells from Lupus patient1 16hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 16hr_BCRFCR
|
| Sample_geo_accession | GSM922059
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922059/suppl/GSM922059_71_316_16hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922060 | GPL201 |
|
72_316_24hr_BCRFCR
|
ebvBcells from Lupus patient1 24hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 24hr_BCRFCR
|
| Sample_geo_accession | GSM922060
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922060/suppl/GSM922060_72_316_24hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922061 | GPL201 |
|
73_100688_0hr_BCRFCR
|
ebvBcells from Lupus patient2 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 0hr_BCRFCR
|
| Sample_geo_accession | GSM922061
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922061/suppl/GSM922061_73_100688_0hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922062 | GPL201 |
|
74_100688_1hr_BCRFCR
|
ebvBcells from Lupus patient2 1hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 1hr_BCRFCR
|
| Sample_geo_accession | GSM922062
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922062/suppl/GSM922062_74_100688_1hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922063 | GPL201 |
|
75_100688_0.5hr_BCRFCR
|
ebvBcells from Lupus patient2 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922063
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922063/suppl/GSM922063_75_100688_.5hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922064 | GPL201 |
|
76_100688_2hr_BCRFCR
|
ebvBcells from Lupus patient2 2hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 2hr_BCRFCR
|
| Sample_geo_accession | GSM922064
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922064/suppl/GSM922064_76_100688_2hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922065 | GPL201 |
|
77_100688_4hr_BCRFCR
|
ebvBcells from Lupus patient2 4hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 4hr_BCRFCR
|
| Sample_geo_accession | GSM922065
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922065/suppl/GSM922065_77_100688_4hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922066 | GPL201 |
|
78_100688_8hr_BCRFCR
|
ebvBcells from Lupus patient2 8hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 8hr_BCRFCR
|
| Sample_geo_accession | GSM922066
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922066/suppl/GSM922066_78_100688_8hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922067 | GPL201 |
|
79_100688_16hr_BCRFCR
|
ebvBcells from Lupus patient2 16hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 16hr_BCRFCR
|
| Sample_geo_accession | GSM922067
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922067/suppl/GSM922067_79_100688_16hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922068 | GPL201 |
|
80_100688_24hr_BCRFCR
|
ebvBcells from Lupus patient2 24hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 24hr_BCRFCR
|
| Sample_geo_accession | GSM922068
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922068/suppl/GSM922068_80_100688_24hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922069 | GPL201 |
|
81_101884_0hr_BCRFCR
|
ebvBcells from Lupus patient1 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 0hr_BCRFCR
|
| Sample_geo_accession | GSM922069
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922069/suppl/GSM922069_81_101884_0hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922070 | GPL201 |
|
82_101884_0.5hr_BCRFCR
|
ebvBcells from Lupus patient1 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922070
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922070/suppl/GSM922070_82_101884_0.5hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922071 | GPL201 |
|
83_101884_1hr_BCRFCR
|
ebvBcells from Lupus patient1 1hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 1hr_BCRFCR
|
| Sample_geo_accession | GSM922071
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922071/suppl/GSM922071_83_101884_1hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922072 | GPL201 |
|
84_101884_2hr_BCRFCR
|
ebvBcells from Lupus patient1 2hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 2hr_BCRFCR
|
| Sample_geo_accession | GSM922072
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922072/suppl/GSM922072_84_101884_2hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922073 | GPL201 |
|
85_101884_4hr_BCRFCR
|
ebvBcells from Lupus patient1 4hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 4hr_BCRFCR
|
| Sample_geo_accession | GSM922073
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922073/suppl/GSM922073_85_101884_4hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922075 | GPL201 |
|
87_101884_16hr_BCRFCR
|
ebvBcells from Lupus patient1 16hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 16hr_BCRFCR
|
| Sample_geo_accession | GSM922075
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922075/suppl/GSM922075_87_101884_16hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922076 | GPL201 |
|
88_101884_24hr_BCRFCR
|
ebvBcells from Lupus patient1 24hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient1 24hr_BCRFCR
|
| Sample_geo_accession | GSM922076
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922076/suppl/GSM922076_88_101884_24hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922077 | GPL201 |
|
89_301948_0hr_BCRFCR
|
ebvBcells from Lupus patient2 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 0hr_BCRFCR
|
| Sample_geo_accession | GSM922077
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922077/suppl/GSM922077_89_301948_0hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922078 | GPL201 |
|
90_301948_0.5hr_BCRFCR
|
ebvBcells from Lupus patient2 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922078
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922078/suppl/GSM922078_90_301948_0.5hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922079 | GPL201 |
|
91_301948_1hr_BCRFCR
|
ebvBcells from Lupus patient2 1hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 1hr_BCRFCR
|
| Sample_geo_accession | GSM922079
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922079/suppl/GSM922079_91_301948_1hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922080 | GPL201 |
|
92_301948_2hr_BCRFCR
|
ebvBcells from Lupus patient2 2hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 2hr_BCRFCR
|
| Sample_geo_accession | GSM922080
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922080/suppl/GSM922080_92_301948_2hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922081 | GPL201 |
|
93_301948_4hr_BCRFCR
|
ebvBcells from Lupus patient2 4hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 4hr_BCRFCR
|
| Sample_geo_accession | GSM922081
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922081/suppl/GSM922081_93_301948_4hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922082 | GPL201 |
|
94_301948_8hr_BCRFCR
|
ebvBcells from Lupus patient2 8hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 8hr_BCRFCR
|
| Sample_geo_accession | GSM922082
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922082/suppl/GSM922082_94_301948_8hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922083 | GPL201 |
|
95_301948_16hr_BCRFCR
|
ebvBcells from Lupus patient2 16hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 16hr_BCRFCR
|
| Sample_geo_accession | GSM922083
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922083/suppl/GSM922083_95_301948_16hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922084 | GPL201 |
|
96_301948_24hr_BCRFCR
|
ebvBcells from Lupus patient2 24hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Lupus patient2 24hr_BCRFCR
|
| Sample_geo_accession | GSM922084
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922084/suppl/GSM922084_96_301948_24hr_BCRFCR.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922085 | GPL201 |
|
32_IgM_0.5_HR_#32
|
ebvBcells from Rep_Lupus patient 4 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 4 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922085
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922085/suppl/GSM922085_32_IgM_0.5_HR__32.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922086 | GPL201 |
|
32_IgM_0_HR_#31
|
ebvBcells from Rep_Lupus patient 4 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 4 0hr_BCRFCR
|
| Sample_geo_accession | GSM922086
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922086/suppl/GSM922086_32_IgM_0_HR__31.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922087 | GPL201 |
|
32_SC_0.5_HR_#30
|
ebvBcells from Rep_Lupus patient 4 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 4 .5hr_serum control
|
| Sample_geo_accession | GSM922087
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922087/suppl/GSM922087_32_SC_0.5_HR__30.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922088 | GPL201 |
|
32_SC_0_HR_#29
|
ebvBcells from Rep_Lupus patient 4 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 4 0hr_serum control
|
| Sample_geo_accession | GSM922088
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922088/suppl/GSM922088_32_SC_0_HR__29.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922089 | GPL201 |
|
45_IgM_0.5_HR_#40
|
ebvBcells from Rep_Lupus patient 6 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 6 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922089
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922089/suppl/GSM922089_45_IgM_0.5_HR__40.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922090 | GPL201 |
|
45_IgM_0_HR_#39
|
ebvBcells from Rep_Lupus patient 6 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 6 0hr_BCRFCR
|
| Sample_geo_accession | GSM922090
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922090/suppl/GSM922090_45_IgM_0_HR__39.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922091 | GPL201 |
|
45_SC_0.5_HR_#38
|
ebvBcells from Rep_Lupus patient 6 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 6 .5hr_serum control
|
| Sample_geo_accession | GSM922091
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922091/suppl/GSM922091_45_SC_0.5_HR__38.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922092 | GPL201 |
|
45_SC_0_HR_#37
|
ebvBcells from Rep_Lupus patient 6 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 6 0hr_serum control
|
| Sample_geo_accession | GSM922092
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922092/suppl/GSM922092_45_SC_0_HR__37.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922093 | GPL201 |
|
349_IgM_0.5_HR_#12
|
ebvBcells from Rep_Lupus patient 1 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 1 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922093
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922093/suppl/GSM922093_349_IgM_0.5_HR__12.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922094 | GPL201 |
|
349_IgM_0_HR_#11
|
ebvBcells from Rep_Lupus patient 1 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 1 0hr_BCRFCR
|
| Sample_geo_accession | GSM922094
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922094/suppl/GSM922094_349_IgM_0_HR__11.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922095 | GPL201 |
|
349_SC_0.5_HR_#10
|
ebvBcells from Rep_Lupus patient 1 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 1 .5hr_serum control
|
| Sample_geo_accession | GSM922095
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922095/suppl/GSM922095_349_SC_0.5_HR__10.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922096 | GPL201 |
|
349_SC_0_HR_#09
|
ebvBcells from Rep_Lupus patient 1 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 1 0hr_serum control
|
| Sample_geo_accession | GSM922096
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922096/suppl/GSM922096_349_SC_0_HR__09.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922097 | GPL201 |
|
100423_IgM_0.5_HR_#36
|
ebvBcells from Rep_Lupus patient 5 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 5 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922097
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922097/suppl/GSM922097_100423_IgM_0.5_HR__36.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922098 | GPL201 |
|
100423_IgM_0_HR_#35
|
ebvBcells from Rep_Lupus patient 5 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 5 0hr_BCRFCR
|
| Sample_geo_accession | GSM922098
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922098/suppl/GSM922098_100423_IgM_0_HR__35.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922099 | GPL201 |
|
100423_SC_0.5_HR_#34
|
ebvBcells from Rep_Lupus patient 5 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 5 .5hr_serum control
|
| Sample_geo_accession | GSM922099
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922099/suppl/GSM922099_100423_SC_0.5_HR__34.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922100 | GPL201 |
|
100423_SC_0_HR_#33
|
ebvBcells from Rep_Lupus patient 5 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 5 0hr_serum control
|
| Sample_geo_accession | GSM922100
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922100/suppl/GSM922100_100423_SC_0_HR__33.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922101 | GPL201 |
|
100450_IgM_0.5_HR_#20
|
ebvBcells from Rep_Lupus patient 2 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 2 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922101
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922101/suppl/GSM922101_100450_IgM_0.5_HR__20.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922102 | GPL201 |
|
100450_IgM_0_HR_#19
|
ebvBcells from Rep_Lupus patient 2 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 2 0hr_BCRFCR
|
| Sample_geo_accession | GSM922102
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922102/suppl/GSM922102_100450_IgM_0_HR__19.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922103 | GPL201 |
|
100450_SC_0.5_HR_#18
|
ebvBcells from Rep_Lupus patient 2 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 2 .5hr_serum control
|
| Sample_geo_accession | GSM922103
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922103/suppl/GSM922103_100450_SC_0.5_HR__18.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922104 | GPL201 |
|
100450_SC_0_HR_#17
|
ebvBcells from Rep_Lupus patient 2 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 2 0hr_serum control
|
| Sample_geo_accession | GSM922104
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922104/suppl/GSM922104_100450_SC_0_HR__17.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922105 | GPL201 |
|
100680_IgM_0.5_HR_#08
|
ebvBcells from Rep_Norm donor 2 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 2 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922105
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922105/suppl/GSM922105_100680_IgM_0.5_HR__08.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922106 | GPL201 |
|
100680_IgM_0_HR_#07
|
ebvBcells from Rep_Norm donor 2 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 2 0hr_BCRFCR
|
| Sample_geo_accession | GSM922106
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922106/suppl/GSM922106_100680_IgM_0_HR__07.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922107 | GPL201 |
|
100680_SC_0.5_HR_#06
|
ebvBcells from Rep_Norm donor 2 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 2 .5hr_serum control
|
| Sample_geo_accession | GSM922107
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922107/suppl/GSM922107_100680_SC_0.5_HR__06.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922108 | GPL201 |
|
100680_SC_0_HR_#05
|
ebvBcells from Rep_Norm donor 2 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 2 0hr_serum control
|
| Sample_geo_accession | GSM922108
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922108/suppl/GSM922108_100680_SC_0_HR__05.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922110 | GPL201 |
|
100850_IgM_0.5_HR_#24
|
ebvBcells from Rep_Lupus patient 3 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 3 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922110
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922110/suppl/GSM922110_100850_IgM_0.5_HR__24.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922111 | GPL201 |
|
100850_IgM_0_HR_#23
|
ebvBcells from Rep_Lupus patient 3 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 3 0hr_BCRFCR
|
| Sample_geo_accession | GSM922111
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922111/suppl/GSM922111_100850_IgM_0_HR__23.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922112 | GPL201 |
|
100850_SC_0.5_HR_#22
|
ebvBcells from Rep_Lupus patient 3 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 3 .5hr_serum control
|
| Sample_geo_accession | GSM922112
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922112/suppl/GSM922112_100850_SC_0.5_HR__22.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922113 | GPL201 |
|
100850_SC_0_HR_#21
|
ebvBcells from Rep_Lupus patient 3 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Systemic Lupus Erythematosus (SLE)
|
ebvBcells from Rep_Lupus patient 3 0hr_serum control
|
| Sample_geo_accession | GSM922113
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922113/suppl/GSM922113_100850_SC_0_HR__21.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922114 | GPL201 |
|
103391_IgM_0.5_HR_#28
|
ebvBcells from Rep_Norm donor 4 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 4 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922114
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922114/suppl/GSM922114_103391_IgM_0.5_HR__28.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922115 | GPL201 |
|
103391_IgM_0_HR_#27
|
ebvBcells from Rep_Norm donor 4 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 4 0hr_BCRFCR
|
| Sample_geo_accession | GSM922115
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922115/suppl/GSM922115_103391_IgM_0_HR__27.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922116 | GPL201 |
|
103391_SC_0.5_HR_#26
|
ebvBcells from Rep_Norm donor 4 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 4 .5hr_serum control
|
| Sample_geo_accession | GSM922116
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922116/suppl/GSM922116_103391_SC_0.5_HR__26.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922117 | GPL201 |
|
103391_SC_0_HR_#25
|
ebvBcells from Rep_Norm donor 4 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 4 0hr_serum control
|
| Sample_geo_accession | GSM922117
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922117/suppl/GSM922117_103391_SC_0_HR__25.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922118 | GPL201 |
|
103538_IgM_0.5_HR_#16
|
ebvBcells from Rep_Norm donor 3 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 3 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922118
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922118/suppl/GSM922118_103538_IgM_0.5_HR__16.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922119 | GPL201 |
|
103538_IgM_0_HR_#15
|
ebvBcells from Rep_Norm donor 3 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 3 0hr_BCRFCR
|
| Sample_geo_accession | GSM922119
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922119/suppl/GSM922119_103538_IgM_0_HR__15.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922120 | GPL201 |
|
103538_SC_0.5_HR_#14
|
ebvBcells from Rep_Norm donor 3 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 3 .5hr_serum control
|
| Sample_geo_accession | GSM922120
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922120/suppl/GSM922120_103538_SC_0.5_HR__14.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922121 | GPL201 |
|
103538_SC_0_HR_#13
|
ebvBcells from Rep_Norm donor 3 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 3 0hr_serum control
|
| Sample_geo_accession | GSM922121
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922121/suppl/GSM922121_103538_SC_0_HR__13.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922122 | GPL201 |
|
301965_IgM_0.5_HR_#04
|
ebvBcells from Rep_Norm donor 1 .5hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 1 .5hr_BCRFCR
|
| Sample_geo_accession | GSM922122
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922122/suppl/GSM922122_301965_IgM_0.5_HR__04.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922123 | GPL201 |
|
301965_IgM_0_HR_#03
|
ebvBcells from Rep_Norm donor 1 0hr_BCRFCR
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 1 0hr_BCRFCR
|
| Sample_geo_accession | GSM922123
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922123/suppl/GSM922123_301965_IgM_0_HR__03.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922124 | GPL201 |
|
301965_SC_0.5_HR_#02
|
ebvBcells from Rep_Norm donor 1 .5hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 1 .5hr_serum control
|
| Sample_geo_accession | GSM922124
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922124/suppl/GSM922124_301965_SC_0.5_HR__02.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
GSM922125 | GPL201 |
|
301965_SC_0_HR_#01
|
ebvBcells from Rep_Norm donor 1 0hr_serum control
|
cell type: Epstein-Barr virus (EBV) transformed B cells
diagnosis: Normal
|
ebvBcells from Rep_Norm donor 1 0hr_serum control
|
| Sample_geo_accession | GSM922125
| | Sample_status | Public on Apr 26 2012
| | Sample_submission_date | Apr 25 2012
| | Sample_last_update_date | Apr 26 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 = CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N | 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol. recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains. B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories. B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with the Qiagen RNeasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| | Sample_hyb_protocol | hybridization to Affymetrix Mouse Genome 430 2.0 arrays.
| | Sample_scan_protocol | scanned on an Affymetrix GeneChip Analysis System GC3000 7G.
| | Sample_data_processing | Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
| | Sample_data_processing | 1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
| | Sample_data_processing | 2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28
| | Sample_platform_id | GPL201
| | Sample_contact_name | Igor,,Dozmorov
| | Sample_contact_email | igor.dozmorov@utsouthwestern.edu
| | Sample_contact_department | Immunology
| | Sample_contact_institute | UT Southwestern Medical Center
| | Sample_contact_address | 5323 Harry Hines Boulevard
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM922nnn/GSM922125/suppl/GSM922125_301965_SC_0_HR__01.CEL.gz
| | Sample_series_id | GSE37573
| | Sample_data_row_count | 8793
| | |
|
| |
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