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Search results for the GEO ID: GSE26669

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GSM656409

GPL1261

CD4 T-Cell Costimulatory blockade treated #1

CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

strain: C57BL/6 cell type: CD4 T-cells agent: leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand

Gene expression data from CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

Sample_geo_accession	GSM656409
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656409/suppl/GSM656409.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656410

GPL1261

CD4 T-Cell Costimulatory blockade treated #2

CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

strain: C57BL/6 cell type: CD4 T-cells agent: leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand

Gene expression data from CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

Sample_geo_accession	GSM656410
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656410/suppl/GSM656410.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656411

GPL1261

CD4 T-Cell no treatment #1

CD4 T-cells isolated from the MLR with nothing additional added to the media

strain: C57BL/6 cell type: CD4 T-cells agent: control

Gene expression data from CD4 T-cells isolated from the MLR with nothing additional added to the media

Sample_geo_accession	GSM656411
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656411/suppl/GSM656411.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656412

GPL1261

CD4 T-Cell no treatment #2

CD4 T-cells isolated from the MLR with nothing additional added to the media

strain: C57BL/6 cell type: CD4 T-cells agent: control

Gene expression data from CD4 T-cells isolated from the MLR with nothing additional added to the media

Sample_geo_accession	GSM656412
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656412/suppl/GSM656412.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656413

GPL1261

CD8 T-Cell Costimulatory blockade treated #1

CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

strain: C57BL/6 cell type: CD8 T-cells agent: leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand

Gene expression data from CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

Sample_geo_accession	GSM656413
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656413/suppl/GSM656413.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656414

GPL1261

CD8 T-Cell Costimulatory blockade treated #2

CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

strain: C57BL/6 cell type: CD8 T-cells agent: leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand

Gene expression data from CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

Sample_geo_accession	GSM656414
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656414/suppl/GSM656414.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656415

GPL1261

CD8 T-Cell no treatment #1

CD8 T-cells isolated from the MLR with nothing additional added to the media

strain: C57BL/6 cell type: CD8 T-cells agent: control

Gene expression data from CD8 T-cells isolated from the MLR with nothing additional added to the media

Sample_geo_accession	GSM656415
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656415/suppl/GSM656415.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

GSM656416

GPL1261

CD8 T-Cell no treatment #2

CD8 T-cells isolated from the MLR with nothing additional added to the media

strain: C57BL/6 cell type: CD8 T-cells agent: control

Gene expression data from CD8 T-cells isolated from the MLR with nothing additional added to the media

Sample_geo_accession	GSM656416
Sample_status	Public on Feb 03 2011
Sample_submission_date	Jan 18 2011
Sample_last_update_date	Feb 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.
Sample_growth_protocol_ch1 = Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n	4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI. Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.
Sample_hyb_protocol	Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with AGCC (Affymetrix Genechip Command Console). Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Kitchener,D.,Wilson
Sample_contact_email	kitchwilson@stanford.edu
Sample_contact_institute	Stanford University
Sample_contact_address	S140 Grant Bldg
Sample_contact_city	Stanford
Sample_contact_state	CA
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM656nnn/GSM656416/suppl/GSM656416.CEL.gz
Sample_series_id	GSE26669
Sample_data_row_count	45101

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