Search results for the GEO ID: GSE16522  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM415024 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated, biological replicate 1
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp1_M-S(+)
|
| Sample_geo_accession | GSM415024
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415024/suppl/GSM415024.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415025 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated, biological replicate 1
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp1_M-S(-)
|
| Sample_geo_accession | GSM415025
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415025/suppl/GSM415025.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415026 | GPL1261 |
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated, biological replicate 1
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: Naïve (CD44-) CD8 T cells
|
exp1_N-S(+)
|
| Sample_geo_accession | GSM415026
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415026/suppl/GSM415026.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415027 | GPL1261 |
|
pmel-1 cd8+ t cells, naive (CD44-), unstimulated, biological replicate 1
|
pmel-1 cd8+ t cells, naive (CD44-), unstimulated
|
genotype: Pmel-1 transgenic mouse
cell type: Naïve (CD44-) CD8 T cells
|
exp1_N-S(-)
|
| Sample_geo_accession | GSM415027
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415027/suppl/GSM415027.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415028 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated biological replicate 2
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp2_M-S(+)
|
| Sample_geo_accession | GSM415028
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415028/suppl/GSM415028.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415029 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated biological replicate 2
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp2_M-S(-)
|
| Sample_geo_accession | GSM415029
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415029/suppl/GSM415029.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415030 | GPL1261 |
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated biological replicate 2
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: Naïve (CD44-) CD8 T cells
|
exp2_N-S(+)
|
| Sample_geo_accession | GSM415030
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415030/suppl/GSM415030.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415031 | GPL1261 |
|
pmel-1 cd8+ t cells, naive (CD44-), unstimulated biological replicate 2
|
pmel-1 cd8+ t cells, naive (CD44-), unstimulated
|
genotype: Pmel-1 transgenic mouse
cell type: Naïve (CD44-) CD8 T cells
|
exp2_N-S(-)
|
| Sample_geo_accession | GSM415031
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415031/suppl/GSM415031.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415032 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated biological replicate 3
|
pmel-1 cd8+ t cells, memory (CD44+), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp3_M-S(+)
|
| Sample_geo_accession | GSM415032
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415032/suppl/GSM415032.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415033 | GPL1261 |
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated, biological replicate 3
|
pmel-1 cd8+ t cells, memory (CD44+), unstimulated
|
genotype: Pmel-1 transgenic mouse
cell type: central memory (CD44+) CD8 T cells
|
exp3_M-S(-)
|
| Sample_geo_accession | GSM415033
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415033/suppl/GSM415033.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
|
GSM415034 | GPL1261 |
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated, biological replicate 3
|
pmel-1 cd8+ t cells, naive (CD44-), stimulated
|
genotype: Pmel-1 transgenic mouse
cell type: Naïve (CD44-) CD8 T cells
|
exp3_N-S(+)
|
| Sample_geo_accession | GSM415034
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 09 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.
| | Sample_growth_protocol_ch1 | Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).
| | Sample_hyb_protocol | Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
| | Sample_data_processing | Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Zachary,,Borman
| | Sample_contact_email | bormanz@mail.nih.gov
| | Sample_contact_phone | 3014518668
| | Sample_contact_laboratory | Nicholas P. Restifo
| | Sample_contact_department | Surgery Branch
| | Sample_contact_institute | National Cancer Institute
| | Sample_contact_address | National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415034/suppl/GSM415034.CEL.gz
| | Sample_series_id | GSE16522
| | Sample_data_row_count | 45101
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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