Search results for the GEO ID: GSE31702  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM786802 | GPL1261 |
|
B6-1
|
CD4+ T cells from B6 mice
|
gender: female
age: 6 months
strain: B6
cell type: CD4+ T cells
|
Gene expression data from B6 CD4+ T cells
|
| Sample_geo_accession | GSM786802
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786802/suppl/GSM786802_4241.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786803 | GPL1261 |
|
B6-2
|
CD4+ T cells from B6 mice
|
gender: female
age: 6 months
strain: B6
cell type: CD4+ T cells
|
Gene expression data from B6 CD4+ T cells
|
| Sample_geo_accession | GSM786803
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786803/suppl/GSM786803_4242.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786804 | GPL1261 |
|
B6-3
|
CD4+ T cells from B6 mice
|
gender: female
age: 6 months
strain: B6
cell type: CD4+ T cells
|
Gene expression data from B6 CD4+ T cells
|
| Sample_geo_accession | GSM786804
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786804/suppl/GSM786804_4243.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786805 | GPL1261 |
|
B6-4
|
CD4+ T cells from B6 mice
|
gender: female
age: 6 months
strain: B6
cell type: CD4+ T cells
|
Gene expression data from B6 CD4+ T cells
|
| Sample_geo_accession | GSM786805
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786805/suppl/GSM786805_4244.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786806 | GPL1261 |
|
B6-5
|
CD4+ T cells from B6 mice
|
gender: female
age: 6 months
strain: B6
cell type: CD4+ T cells
|
Gene expression data from B6 CD4+ T cells
|
| Sample_geo_accession | GSM786806
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786806/suppl/GSM786806_4245.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786807 | GPL1261 |
|
REC5-1
|
CD4+ T cells from B6.Sle1c2 mice
|
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Sample_geo_accession | GSM786807
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786807/suppl/GSM786807_4246.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786808 | GPL1261 |
|
REC5-2
|
CD4+ T cells from B6.Sle1c2 mice
|
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Sample_geo_accession | GSM786808
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786808/suppl/GSM786808_4247.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786809 | GPL1261 |
|
REC5-3
|
CD4+ T cells from B6.Sle1c2 mice
|
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Sample_geo_accession | GSM786809
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786809/suppl/GSM786809_4248.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786810 | GPL1261 |
|
REC5-4
|
CD4+ T cells from B6.Sle1c2 mice
|
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Sample_geo_accession | GSM786810
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786810/suppl/GSM786810_4249.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
GSM786811 | GPL1261 |
|
REC5-5
|
CD4+ T cells from B6.Sle1c2 mice
|
gender: female
age: 6 months
strain: B6.Sle1c2
cell type: CD4+ T cells
|
Gene expression data from B6.Sle1c2 CD4+ T cells
|
| Sample_geo_accession | GSM786811
| | Sample_status | Public on Aug 30 2011
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Aug 30 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).
| | Sample_growth_protocol_ch1 | Female mice aged 6 months under SPF conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Rneasy kits (Qiagen).
| | 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 | Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)
| | Sample_data_processing | The microarray data analysis was based on the use of “internal standards” (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf. Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69. Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11. Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39. Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Laurence,M,Morel
| | Sample_contact_email | morel@ufl.edu
| | Sample_contact_laboratory | Morel Lab
| | Sample_contact_department | Pathology, Immunology and Laboratory Medicine
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | PO Box 100275
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786811/suppl/GSM786811_4250.CEL.gz
| | Sample_series_id | GSE31702
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
