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Search results for the GEO ID: GSE43635

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GSM1067396

GPL1261

Affy Clip Syn-T cells biological rep 1

T cells co-cultured with syngeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with syngeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Syn-T cells

Sample_geo_accession	GSM1067396
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067396/suppl/GSM1067396_Affy_Clip-Syn-T_Cell-1.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067397

GPL1261

Affy Clip Syn-T cells biological rep 2

T cells co-cultured with syngeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with syngeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Syn-T cells

Sample_geo_accession	GSM1067397
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067397/suppl/GSM1067397_Affy_Clip-Syn-T_Cell-2.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067398

GPL1261

Affy ClipSyn-T cells biological rep 3

T cells co-cultured with syngeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with syngeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Syn-T cells

Sample_geo_accession	GSM1067398
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067398/suppl/GSM1067398_Affy_Clip-Syn-T_Cell-3.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067399

GPL1261

Affy ClipAllo-T cells biological rep 1

T cells co-cultured with allongeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with allongeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Allo-T cells

Sample_geo_accession	GSM1067399
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067399/suppl/GSM1067399_Affy_Clip-Allo-T_Cell-1.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067400

GPL1261

Affy ClipAllo-T cells biological rep 2

T cells co-cultured with allongeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with allongeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Allo-T cells

Sample_geo_accession	GSM1067400
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067400/suppl/GSM1067400_Affy_Clip-Allo-T_Cell-2.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067401

GPL1261

Affy ClipAllo-T cells biological rep 3

T cells co-cultured with allongeneic dendritic cells

strain: C57BL/6 cell type: T lymphocytes treatment: T cells co-cultured with allongeneic dendritic cells clip antibody: AGO

AGO-Clip Enriched transcripts from Allo-T cells

Sample_geo_accession	GSM1067401
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067401/suppl/GSM1067401_Affy_Clip-Allo-T_Cell-3.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067402

GPL1261

Affy ClipCD3-28-T cells biological rep 1

T cells cultivated with anti-CD3e and anti-CD28 mAB9

strain: C57BL/6 cell type: T lymphocytes treatment: T cells cultivated with anti-CD3e and anti-CD28 mAB9 clip antibody: AGO

AGO-Clip Enriched transcripts from CD3-CD28 antibody activated T cells

Sample_geo_accession	GSM1067402
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067402/suppl/GSM1067402_Affy_Clip-CD3-28-T_Cell-1.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067403

GPL1261

Affy ClipCD3-28-T cells biological rep 2

T cells cultivated with anti-CD3e and anti-CD28 mAB9

strain: C57BL/6 cell type: T lymphocytes treatment: T cells cultivated with anti-CD3e and anti-CD28 mAB9 clip antibody: AGO

AGO-Clip Enriched transcripts from CD3-CD28 antibody activated T cells

Sample_geo_accession	GSM1067403
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067403/suppl/GSM1067403_Affy_Clip-CD3-28-T_Cell-2.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

GSM1067404

GPL1261

Affy ClipCD3-28-T cells biological rep 3

T cells cultivated with anti-CD3e and anti-CD28 mAB9

strain: C57BL/6 cell type: T lymphocytes treatment: T cells cultivated with anti-CD3e and anti-CD28 mAB9 clip antibody: AGO

AGO-Clip Enriched transcripts from CD3-CD28 antibody activated T cells

Sample_geo_accession	GSM1067404
Sample_status	Public on Jan 19 2013
Sample_submission_date	Jan 18 2013
Sample_last_update_date	Jan 19 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2 from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.
Sample_growth_protocol_ch1	Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed using WT-Ovation™ Pico System ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.
Sample_data_processing	Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.
Sample_platform_id	GPL1261
Sample_contact_name	yaping,,sun
Sample_contact_email	yapings@umich.edu
Sample_contact_phone	7346157127
Sample_contact_fax	7346479747
Sample_contact_department	internal medicine
Sample_contact_institute	university of michigan
Sample_contact_address	1500 E Medical Center Dr.
Sample_contact_city	Ann Arbor
Sample_contact_state	Michigan
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1067nnn/GSM1067404/suppl/GSM1067404_Affy_Clip-CD3-28-T_Cell-3.CEL.gz
Sample_series_id	GSE43635
Sample_series_id	GSE43636
Sample_data_row_count	45101

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