Search results for the GEO ID: GSE20081  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM503878 | GPL570 |
|
HeLa_NT siRNA_rep1
|
HeLa cells,control
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: control siRNA
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503878
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503878/suppl/GSM503878.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503879 | GPL570 |
|
HeLa_NT siRNA_rep2
|
HeLa cells,control
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: control siRNA
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503879
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503879/suppl/GSM503879.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503880 | GPL570 |
|
HeLa_NT siRNA_rep3
|
HeLa cells,control
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: control siRNA
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503880
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503880/suppl/GSM503880.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503881 | GPL570 |
|
HeLa_SRA siRNA_rep1
|
HeLa cells, SRA siRNA
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: siRNA-mediated SRA depletion
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503881
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503881/suppl/GSM503881.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503882 | GPL570 |
|
HeLa_SRA siRNA_rep2
|
HeLa cells, SRA siRNA
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: siRNA-mediated SRA depletion
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503882
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503882/suppl/GSM503882.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503883 | GPL570 |
|
HeLa_SRA siRNA_rep3
|
HeLa cells, SRA siRNA
|
cell line: HeLa cancer cell line
tissue origin of cancer cell: cervix
protocol: siRNA-mediated SRA depletion
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503883
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503883/suppl/GSM503883.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503884 | GPL570 |
|
MCF-7_minus E2_NT siRNA_rep1
|
MCF-7 cells minus E2,control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503884
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503884/suppl/GSM503884.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503885 | GPL570 |
|
MCF-7_minus E2_NT siRNA_rep2
|
MCF-7 cells minus E2,control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503885
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503885/suppl/GSM503885.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503886 | GPL570 |
|
MCF-7_minus E2_NT siRNA_rep3
|
MCF-7 cells minus E2,control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503886
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503886/suppl/GSM503886.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503887 | GPL570 |
|
MCF-7_10 nM E2 (6h)_NT siRNA_rep1
|
MCF-7 cells 10 nM E2 (6h),control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503887
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503887/suppl/GSM503887.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503888 | GPL570 |
|
MCF-7_10 nM E2 (6h)_NT siRNA_rep2
|
MCF-7 cells 10 nM E2 (6h),control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503888
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503888/suppl/GSM503888.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503889 | GPL570 |
|
MCF-7_10 nM E2 (6h)_NT siRNA_rep3
|
MCF-7 cells 10 nM E2 (6h),control
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: control siRNA
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503889
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503889/suppl/GSM503889.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503890 | GPL570 |
|
MCF-7_minus E2_SRA siRNA_rep1
|
MCF-7 cells minus E2, SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503890
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503890/suppl/GSM503890.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503891 | GPL570 |
|
MCF-7_minus E2_SRA siRNA_rep2
|
MCF-7 cells minus E2, SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503891
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503891/suppl/GSM503891.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503892 | GPL570 |
|
MCF-7_minus E2_SRA siRNA_rep3
|
MCF-7 cells minus E2, SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: no estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503892
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503892/suppl/GSM503892.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503893 | GPL570 |
|
MCF-7_10 nM E2 (6h)_SRA siRNA_rep1
|
MCF-7 cells 10 nM E2 (6h), SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503893
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503893/suppl/GSM503893.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503894 | GPL570 |
|
MCF-7_10 nM E2 (6h)_SRA siRNA_rep2
|
MCF-7 cells 10 nM E2 (6h), SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503894
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503894/suppl/GSM503894.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
GSM503895 | GPL570 |
|
MCF-7_10 nM E2 (6h)_SRA siRNA_rep3
|
MCF-7 cells 10 nM E2 (6h), SRA siRNA
|
cell line: MCF-7 cancer cell line
tissue origin of cancer cell: breast
protocol: siRNA-mediated SRA depletion
agent: estradiol
|
Affymetrix HG U133+2 data
|
| Sample_geo_accession | GSM503895
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 01 2010
| | Sample_last_update_date | Feb 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.
| | Sample_growth_protocol_ch1 | HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop spectrophotometer.
| | Sample_hyb_protocol | 15 ug of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array. The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated anti-streptavidin.
| | Sample_scan_protocol | The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.
| | Sample_data_processing | We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Charles,E,Foulds
| | Sample_contact_email | foulds@bcm.edu
| | Sample_contact_phone | 713-798-6247
| | Sample_contact_fax | 713-790-1275
| | Sample_contact_laboratory | Bert W. O'Malley
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM503nnn/GSM503895/suppl/GSM503895.cel.gz
| | Sample_series_id | GSE20081
| | Sample_data_row_count | 54675
| | |
|
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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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