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Search results for the GEO ID: GSE22313

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Title

Source name

Description

Characteristics

GSM555381

GPL1261

B6 Control R1

CD4+ T cells from B6 mice

strain: C57BL/6 genotype/variation: wild type gender: female sample type: control

control B1a replicate 1

Sample_geo_accession	GSM555381
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555381/suppl/GSM555381.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555382

GPL1261

B6 Control R2

CD4+ T cells from B6 mice

strain: C57BL/6 genotype/variation: wild type gender: female sample type: control

control B1a replicate 2

Sample_geo_accession	GSM555382
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555382/suppl/GSM555382.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555383

GPL1261

B6 Control R3

CD4+ T cells from B6 mice

strain: C57BL/6 genotype/variation: wild type gender: female sample type: control

control B1a replicate 3

Sample_geo_accession	GSM555383
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555383/suppl/GSM555383.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555384

GPL1261

B6 Control R4

CD4+ T cells from B6 mice

strain: C57BL/6 genotype/variation: wild type gender: female sample type: control

control B1a replicate 4

Sample_geo_accession	GSM555384
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555384/suppl/GSM555384.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555385

GPL1261

Sle1a R1

CD4+ T cells from B6.Sle1a.1 mice

strain: C57BL/6 genotype/variation: B6.Sle1a.1 gender: female sample type: experimental

exp B1a replicate 1

Sample_geo_accession	GSM555385
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555385/suppl/GSM555385.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555386

GPL1261

Sle1a R2

CD4+ T cells from B6.Sle1a.1 mice

strain: C57BL/6 genotype/variation: B6.Sle1a.1 gender: female sample type: experimental

exp B1a replicate 2

Sample_geo_accession	GSM555386
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555386/suppl/GSM555386.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555387

GPL1261

Sle1a R3

CD4+ T cells from B6.Sle1a.1 mice

strain: C57BL/6 genotype/variation: B6.Sle1a.1 gender: female sample type: experimental

exp B1a replicate 3

Sample_geo_accession	GSM555387
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555387/suppl/GSM555387.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

GSM555388

GPL1261

Sle1a R4

CD4+ T cells from B6.Sle1a.1 mice

strain: C57BL/6 genotype/variation: B6.Sle1a.1 gender: female sample type: experimental

exp B1a replicate 4

Sample_geo_accession	GSM555388
Sample_status	Public on Jun 16 2010
Sample_submission_date	Jun 11 2010
Sample_last_update_date	Jun 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
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	All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Sample_data_processing	Two-step normalization procedure (1). 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”. The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
Sample_data_processing	1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.
Sample_platform_id	GPL1261
Sample_contact_name	Igor,M,Dozmorov
Sample_contact_email	igor-dozmorov@omrf.org
Sample_contact_phone	405-271-7052
Sample_contact_fax	405-271-7063
Sample_contact_department	Arthritis & Immunology
Sample_contact_institute	OMRF
Sample_contact_address	825 NE 13th Street
Sample_contact_city	Oklahoma City
Sample_contact_state	OK
Sample_contact_zip/postal_code	73162
Sample_contact_country	USA
Sample_contact_web_link	omrf.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM555nnn/GSM555388/suppl/GSM555388.CEL.gz
Sample_series_id	GSE22313
Sample_data_row_count	45101

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