Result

Search results for the GEO ID: GSE32624

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GSM ID

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Title

Source name

Description

Characteristics

GSM808728

GPL1261

K.L_07_WT-Tfh-like

Primary CD4+ T cells

strain: WT TCR transgenic OT-II tissue: spleen and lymph nodes cell type: WT in vitro generated Tfh-like cells

Sample_geo_accession	GSM808728
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808728/suppl/GSM808728_K.L_07_WT-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808728/suppl/GSM808728_KL_07_WT-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

GSM808729

GPL1261

K.L_08_WT-Tfh-like

Primary CD4+ T cells

strain: WT TCR transgenic OT-II tissue: spleen and lymph nodes cell type: WT in vitro generated Tfh-like cells

Sample_geo_accession	GSM808729
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808729/suppl/GSM808729_K.L_08_WT-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808729/suppl/GSM808729_KL_08_WT-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

GSM808730

GPL1261

K.L_09_WT-Tfh-like

Primary CD4+ T cells

strain: WT TCR transgenic OT-II tissue: spleen and lymph nodes cell type: WT in vitro generated Tfh-like cells

Sample_geo_accession	GSM808730
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808730/suppl/GSM808730_K.L_09_WT-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808730/suppl/GSM808730_KL_09_WT-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

GSM808731

GPL1261

KL_10_SAP-Tfh-like

Primary CD4+ T cells

strain: SAP-deficient TCR transgenic OT-II tissue: spleen and lymph nodes cell type: SAP-deficient in vitro generated Tfh-like cells

Sample_geo_accession	GSM808731
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808731/suppl/GSM808731_K.L_10_SAP-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808731/suppl/GSM808731_KL_10_SAP-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

GSM808732

GPL1261

KL_11_SAP-Tfh-like

Primary CD4+ T cells

strain: SAP-deficient TCR transgenic OT-II tissue: spleen and lymph nodes cell type: SAP-deficient in vitro generated Tfh-like cells

Sample_geo_accession	GSM808732
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808732/suppl/GSM808732_K.L_11_SAP-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808732/suppl/GSM808732_KL_11_SAP-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

GSM808733

GPL1261

KL_12_SAP-Tfh-like

Primary CD4+ T cells

strain: SAP-deficient TCR transgenic OT-II tissue: spleen and lymph nodes cell type: SAP-deficient in vitro generated Tfh-like cells

Sample_geo_accession	GSM808733
Sample_status	Public on Dec 06 2011
Sample_submission_date	Oct 05 2011
Sample_last_update_date	Dec 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting. Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).
Sample_label_ch1	biotin-streptavidin
Sample_label_protocol_ch1	500 ng of total RNA was used for labeling with the Illumina total prep kit. The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
Sample_hyb_protocol	The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Sample_scan_protocol	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
Sample_data_processing	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
Sample_platform_id	GPL1261
Sample_contact_name	abdel,G,Elkahloun
Sample_contact_email	abdel@mail.nih.gov
Sample_contact_phone	301 402 3170
Sample_contact_laboratory	MICROARRAY CORE
Sample_contact_institute	NHGRI-NIH
Sample_contact_address	50, SOUTH DRIVE
Sample_contact_city	BETHESDA
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808733/suppl/GSM808733_K.L_12_SAP-Tfh-like.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM808nnn/GSM808733/suppl/GSM808733_KL_12_SAP-Tfh-like.chp.gz
Sample_series_id	GSE32624
Sample_data_row_count	45101

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