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Search results for the GEO ID: GSE43936

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Description

Characteristics

GSM1074697

GPL1261

T cells_empty virus transduced_stimulated_6 hours_rep1

T cells_empty virus_stimulated 6hrs

strain background: C57BL/6 genotype/variation: CAR Tg x PTENflox/flox cell type: peripheral CD4 T cells transduced with: adeno-EV (empty virus) at x100 MOI for 1h stimulated with: anti-CD3/anti-CD28 mAb-coated beads for 6hrs

CD4 T cell clones transfected with empty virus then washed and expanded then stimulated for 6 hours and evaluated exp1_Ev6; Ev6-1

Sample_geo_accession	GSM1074697
Sample_status	Public on Feb 01 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Feb 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	T cells were activated with beads (Dynal) coated overnight at 4 degrees with anti-CD3 (145-2C11) at 1 microg/ml and anti-CD28 (PV1) at 1 microg/ml. For stimulation, T cells were incubated with the antibody-coated beads in 24 well plates at 1x10 6 cells/well in 1 ml for 6 hours at 37°C at a 5:1 bead to T cell ratio.
Sample_growth_protocol_ch1	For adenoviral transduction, peripheral CAR Tg x PTENflox/flox T cells (total, CD4+, or CD8+) were isolated from splenocytes by negative selection with MACS antibody cocktails and magnetic beads (Miltenyi Biotec). Transduced CAR Tg x PTENflox/flox Th1 clones were rested overnight and then passaged under normal conditions, and 9 days later clones were harvested for experiments.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by TRIzol reagent protocol (Invitrogen), followed by RNeasy Mini column purification (QIAGEN) according to manufacturer's instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). The concentration/purity was determined using a NanoDrop 1000 (Thermo Scientific). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and RIN (RNA Integrity Number) > 8.0.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was processed to cDNA synthesis, cRNA synthesis, fragmentation, and hybridization to expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc). Briefly, 2 ug of total RNA was used to synthesize double-stranded cDNA using the Genechip Expression 3´ -Amplification one cycle cDNA Synthesis kit (Affymetrix). First strand cDNA synthesis was primed with a oligo(dT)24 primer that contains T7 promoter sequences. From the cDNA purified by Genechip sample cleanup module (Affymetrix), biotin-labeled antisense RNA (cRNA) was synthesized using Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).
Sample_hyb_protocol	After cleanup of cRNA with Genechip sample cleanup module, 20 µg of cRNA was fragmented in fragmentation buffer for 35 min at 94°C. The fragmented cRNA (12 µg) was hybridized to Affymetrix MG 430 2.0 expression arrays for 16 h at 45°C and 60 rpm in an affymetrix hybridization oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.
Sample_scan_protocol	Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G. CEL intensity files generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0) were used to extract and analyze data using dChip software (Harvard).
Sample_data_processing	Array normalization and expression value calculation were performed uisng dchip_2020_01 (v.1.0.0.1). Each analysis was done in duplicate utilizing different primary material treated with equivalent experimental conditions. Arrays were normalized at the probe cell level by the invariant set normalization method to allow for comparison of expression values computed using the model-based method.
Sample_data_processing	Measurement accuracy evaluated by standard error was used to compute 90% confidence intervals of fold changes in two sample and two-group comparisons (ie: EV to Cre comparison done twice and compared for consistency). Increased or decreased expression of genes by more than 2-fold (lower confidence bound) are presented ['fold_change_data.txt' on Series records].
Sample_platform_id	GPL1261
Sample_contact_name	yuanyuan,,zha
Sample_contact_email	yzha@uchicago.edu
Sample_contact_phone	772-702-4812
Sample_contact_fax	773-702-7195
Sample_contact_department	Department of Pathology
Sample_contact_institute	University of Chicago
Sample_contact_address	910 E. 58th St. MKL051
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1074nnn/GSM1074697/suppl/GSM1074697_exp1_Ev6.CEL.gz
Sample_series_id	GSE43936
Sample_data_row_count	45037

GSM1074698

GPL1261

T cells_Cre virus transduced_stimulated_6 hours_rep1

T cells_Cre virus_stimulated 6hrs

strain background: C57BL/6 genotype/variation: CAR Tg x PTENflox/flox cell type: peripheral CD4 T cells transduced with: adeno-Cre at x100 MOI for 1h stimulated with: anti-CD3/anti-CD28 mAb-coated beads for 6hrs

CD4 T cell clones transfected with Cre virus then washed and expanded then stimulated for 6 hours then evaluated exp1_Cre6; Cre6-1

Sample_geo_accession	GSM1074698
Sample_status	Public on Feb 01 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Feb 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	T cells were activated with beads (Dynal) coated overnight at 4 degrees with anti-CD3 (145-2C11) at 1 microg/ml and anti-CD28 (PV1) at 1 microg/ml. For stimulation, T cells were incubated with the antibody-coated beads in 24 well plates at 1x10 6 cells/well in 1 ml for 6 hours at 37°C at a 5:1 bead to T cell ratio.
Sample_growth_protocol_ch1	For adenoviral transduction, peripheral CAR Tg x PTENflox/flox T cells (total, CD4+, or CD8+) were isolated from splenocytes by negative selection with MACS antibody cocktails and magnetic beads (Miltenyi Biotec). Transduced CAR Tg x PTENflox/flox Th1 clones were rested overnight and then passaged under normal conditions, and 9 days later clones were harvested for experiments.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by TRIzol reagent protocol (Invitrogen), followed by RNeasy Mini column purification (QIAGEN) according to manufacturer's instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). The concentration/purity was determined using a NanoDrop 1000 (Thermo Scientific). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and RIN (RNA Integrity Number) > 8.0.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was processed to cDNA synthesis, cRNA synthesis, fragmentation, and hybridization to expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc). Briefly, 2 ug of total RNA was used to synthesize double-stranded cDNA using the Genechip Expression 3´ -Amplification one cycle cDNA Synthesis kit (Affymetrix). First strand cDNA synthesis was primed with a oligo(dT)24 primer that contains T7 promoter sequences. From the cDNA purified by Genechip sample cleanup module (Affymetrix), biotin-labeled antisense RNA (cRNA) was synthesized using Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).
Sample_hyb_protocol	After cleanup of cRNA with Genechip sample cleanup module, 20 µg of cRNA was fragmented in fragmentation buffer for 35 min at 94°C. The fragmented cRNA (12 µg) was hybridized to Affymetrix MG 430 2.0 expression arrays for 16 h at 45°C and 60 rpm in an affymetrix hybridization oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.
Sample_scan_protocol	Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G. CEL intensity files generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0) were used to extract and analyze data using dChip software (Harvard).
Sample_data_processing	Array normalization and expression value calculation were performed uisng dchip_2020_01 (v.1.0.0.1). Each analysis was done in duplicate utilizing different primary material treated with equivalent experimental conditions. Arrays were normalized at the probe cell level by the invariant set normalization method to allow for comparison of expression values computed using the model-based method.
Sample_data_processing	Measurement accuracy evaluated by standard error was used to compute 90% confidence intervals of fold changes in two sample and two-group comparisons (ie: EV to Cre comparison done twice and compared for consistency). Increased or decreased expression of genes by more than 2-fold (lower confidence bound) are presented ['fold_change_data.txt' on Series records].
Sample_platform_id	GPL1261
Sample_contact_name	yuanyuan,,zha
Sample_contact_email	yzha@uchicago.edu
Sample_contact_phone	772-702-4812
Sample_contact_fax	773-702-7195
Sample_contact_department	Department of Pathology
Sample_contact_institute	University of Chicago
Sample_contact_address	910 E. 58th St. MKL051
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1074nnn/GSM1074698/suppl/GSM1074698_exp1_Cre6.CEL.gz
Sample_series_id	GSE43936
Sample_data_row_count	45037

GSM1074699

GPL1261

T cells_empty virus transduced_stimulated_6 hours_rep2

T cells_empty virus_stimulated 6hrs

CD4 T cell clones transfected with empty virus then washed and expanded then stimulated for 6 hours and evaluated exp2_EV 6; EV 6-2

Sample_geo_accession	GSM1074699
Sample_status	Public on Feb 01 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Feb 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	T cells were activated with beads (Dynal) coated overnight at 4 degrees with anti-CD3 (145-2C11) at 1 microg/ml and anti-CD28 (PV1) at 1 microg/ml. For stimulation, T cells were incubated with the antibody-coated beads in 24 well plates at 1x10 6 cells/well in 1 ml for 6 hours at 37°C at a 5:1 bead to T cell ratio.
Sample_growth_protocol_ch1	For adenoviral transduction, peripheral CAR Tg x PTENflox/flox T cells (total, CD4+, or CD8+) were isolated from splenocytes by negative selection with MACS antibody cocktails and magnetic beads (Miltenyi Biotec). Transduced CAR Tg x PTENflox/flox Th1 clones were rested overnight and then passaged under normal conditions, and 9 days later clones were harvested for experiments.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by TRIzol reagent protocol (Invitrogen), followed by RNeasy Mini column purification (QIAGEN) according to manufacturer's instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). The concentration/purity was determined using a NanoDrop 1000 (Thermo Scientific). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and RIN (RNA Integrity Number) > 8.0.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was processed to cDNA synthesis, cRNA synthesis, fragmentation, and hybridization to expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc). Briefly, 2 ug of total RNA was used to synthesize double-stranded cDNA using the Genechip Expression 3´ -Amplification one cycle cDNA Synthesis kit (Affymetrix). First strand cDNA synthesis was primed with a oligo(dT)24 primer that contains T7 promoter sequences. From the cDNA purified by Genechip sample cleanup module (Affymetrix), biotin-labeled antisense RNA (cRNA) was synthesized using Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).
Sample_hyb_protocol	After cleanup of cRNA with Genechip sample cleanup module, 20 µg of cRNA was fragmented in fragmentation buffer for 35 min at 94°C. The fragmented cRNA (12 µg) was hybridized to Affymetrix MG 430 2.0 expression arrays for 16 h at 45°C and 60 rpm in an affymetrix hybridization oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.
Sample_scan_protocol	Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G. CEL intensity files generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0) were used to extract and analyze data using dChip software (Harvard).
Sample_data_processing	Array normalization and expression value calculation were performed uisng dchip_2020_01 (v.1.0.0.1). Each analysis was done in duplicate utilizing different primary material treated with equivalent experimental conditions. Arrays were normalized at the probe cell level by the invariant set normalization method to allow for comparison of expression values computed using the model-based method.
Sample_data_processing	Measurement accuracy evaluated by standard error was used to compute 90% confidence intervals of fold changes in two sample and two-group comparisons (ie: EV to Cre comparison done twice and compared for consistency). Increased or decreased expression of genes by more than 2-fold (lower confidence bound) are presented ['fold_change_data.txt' on Series records].
Sample_platform_id	GPL1261
Sample_contact_name	yuanyuan,,zha
Sample_contact_email	yzha@uchicago.edu
Sample_contact_phone	772-702-4812
Sample_contact_fax	773-702-7195
Sample_contact_department	Department of Pathology
Sample_contact_institute	University of Chicago
Sample_contact_address	910 E. 58th St. MKL051
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1074nnn/GSM1074699/suppl/GSM1074699_exp2_EV_6.CEL.gz
Sample_series_id	GSE43936
Sample_data_row_count	45037

GSM1074700

GPL1261

T cells_Cre virus transduced_stimulated_6 hours_rep2

T cells_Cre virus_stimulated 6hrs

CD4 T cell clones transfected with Cre virus then washed and expanded then stimulated for 6 hours then evaluated exp2_Cre6; Cre 6-2

Sample_geo_accession	GSM1074700
Sample_status	Public on Feb 01 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Feb 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	T cells were activated with beads (Dynal) coated overnight at 4 degrees with anti-CD3 (145-2C11) at 1 microg/ml and anti-CD28 (PV1) at 1 microg/ml. For stimulation, T cells were incubated with the antibody-coated beads in 24 well plates at 1x10 6 cells/well in 1 ml for 6 hours at 37°C at a 5:1 bead to T cell ratio.
Sample_growth_protocol_ch1	For adenoviral transduction, peripheral CAR Tg x PTENflox/flox T cells (total, CD4+, or CD8+) were isolated from splenocytes by negative selection with MACS antibody cocktails and magnetic beads (Miltenyi Biotec). Transduced CAR Tg x PTENflox/flox Th1 clones were rested overnight and then passaged under normal conditions, and 9 days later clones were harvested for experiments.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by TRIzol reagent protocol (Invitrogen), followed by RNeasy Mini column purification (QIAGEN) according to manufacturer's instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). The concentration/purity was determined using a NanoDrop 1000 (Thermo Scientific). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and RIN (RNA Integrity Number) > 8.0.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was processed to cDNA synthesis, cRNA synthesis, fragmentation, and hybridization to expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc). Briefly, 2 ug of total RNA was used to synthesize double-stranded cDNA using the Genechip Expression 3´ -Amplification one cycle cDNA Synthesis kit (Affymetrix). First strand cDNA synthesis was primed with a oligo(dT)24 primer that contains T7 promoter sequences. From the cDNA purified by Genechip sample cleanup module (Affymetrix), biotin-labeled antisense RNA (cRNA) was synthesized using Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).
Sample_hyb_protocol	After cleanup of cRNA with Genechip sample cleanup module, 20 µg of cRNA was fragmented in fragmentation buffer for 35 min at 94°C. The fragmented cRNA (12 µg) was hybridized to Affymetrix MG 430 2.0 expression arrays for 16 h at 45°C and 60 rpm in an affymetrix hybridization oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.
Sample_scan_protocol	Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G. CEL intensity files generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0) were used to extract and analyze data using dChip software (Harvard).
Sample_data_processing	Array normalization and expression value calculation were performed uisng dchip_2020_01 (v.1.0.0.1). Each analysis was done in duplicate utilizing different primary material treated with equivalent experimental conditions. Arrays were normalized at the probe cell level by the invariant set normalization method to allow for comparison of expression values computed using the model-based method.
Sample_data_processing	Measurement accuracy evaluated by standard error was used to compute 90% confidence intervals of fold changes in two sample and two-group comparisons (ie: EV to Cre comparison done twice and compared for consistency). Increased or decreased expression of genes by more than 2-fold (lower confidence bound) are presented ['fold_change_data.txt' on Series records].
Sample_platform_id	GPL1261
Sample_contact_name	yuanyuan,,zha
Sample_contact_email	yzha@uchicago.edu
Sample_contact_phone	772-702-4812
Sample_contact_fax	773-702-7195
Sample_contact_department	Department of Pathology
Sample_contact_institute	University of Chicago
Sample_contact_address	910 E. 58th St. MKL051
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1074nnn/GSM1074700/suppl/GSM1074700_exp2_Cre6.CEL.gz
Sample_series_id	GSE43936
Sample_data_row_count	45037

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