Search results for the GEO ID: GSE38232  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM937089 | GPL3921 |
|
HMLER Scramble Rep1
|
HMLER cells
|
cell line: HMLER
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from HMLER cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937089
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937089/suppl/GSM937089_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E07_440120.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937090 | GPL3921 |
|
HMLER Scramble Rep2
|
HMLER cells
|
cell line: HMLER
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from HMLER cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937090
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937090/suppl/GSM937090_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E08_440122.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937091 | GPL3921 |
|
HMLER GFP Rep1
|
HMLER cells
|
cell line: HMLER
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from HMLER cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937091
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937091/suppl/GSM937091_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E05_440124.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937092 | GPL3921 |
|
HMLER GFP Rep2
|
HMLER cells
|
cell line: HMLER
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from HMLER cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937092
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937092/suppl/GSM937092_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E06_440126.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937093 | GPL3921 |
|
HMLER hA6 Rep1
|
HMLER cells
|
cell line: HMLER
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from HMLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937093
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937093/suppl/GSM937093_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E01_440132.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937094 | GPL3921 |
|
HMLER hA6 Rep2
|
HMLER cells
|
cell line: HMLER
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from HMLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937094
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937094/suppl/GSM937094_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E02_440134.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937095 | GPL3921 |
|
BPLER Scramble Rep1
|
BPLER cells
|
cell line: BPLER
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from BPLER cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937095
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937095/suppl/GSM937095_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B07_440254.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937096 | GPL3921 |
|
BPLER Scramble Rep2
|
BPLER cells
|
cell line: BPLER
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from BPLER cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937096
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937096/suppl/GSM937096_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B08_440252.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937097 | GPL3921 |
|
BPLER GFP Rep1
|
BPLER cells
|
cell line: BPLER
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from BPLER cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937097
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937097/suppl/GSM937097_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B05_440250.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937098 | GPL3921 |
|
BPLER GFP Rep2
|
BPLER cells
|
cell line: BPLER
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from BPLER cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937098
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937098/suppl/GSM937098_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B06_440248.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937099 | GPL3921 |
|
BPLER hA6 Rep1
|
BPLER cells
|
cell line: BPLER
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from BPLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937099
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937099/suppl/GSM937099_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B01_440242.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937100 | GPL3921 |
|
BPLER hA6 Rep2
|
BPLER cells
|
cell line: BPLER
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from BPLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937100
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937100/suppl/GSM937100_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B02_440240.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937101 | GPL3921 |
|
MCF7 Scramble Rep1
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from MCF7 cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937101
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937101/suppl/GSM937101_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A07_440192.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937102 | GPL3921 |
|
MCF7 Scramble Rep2
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with a scramble control lentiviral shRNAi
|
Gene expression data from MCF7 cells transduced with a scramble control lentiviral shRNAi
|
| Sample_geo_accession | GSM937102
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937102/suppl/GSM937102_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A08_440194.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937103 | GPL3921 |
|
MCF7 GFP Rep1
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from MCF7 cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937103
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937103/suppl/GSM937103_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A05_440196.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937104 | GPL3921 |
|
MCF7 GFP Rep2
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with a scramble control GFP shRNAi
|
Gene expression data from MCF7 cells transduced with a scramble control GFP shRNAi
|
| Sample_geo_accession | GSM937104
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937104/suppl/GSM937104_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A06_440198.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937105 | GPL3921 |
|
MCF7 hA6 Rep1
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from MCF7 cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937105
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937105/suppl/GSM937105_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A01_440188.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937106 | GPL3921 |
|
MCF7 hA6 Rep2
|
MCF7 cells
|
cell line: MCF7
treatment: transduced with hA6 lentiviral shRNAi to deplete HSF1
|
Gene expression data from MCF7 cells transduced with hA6 lentiviral shRNAi to deplete HSF1
|
| Sample_geo_accession | GSM937106
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937106/suppl/GSM937106_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_A02_440190.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937107 | GPL3921 |
|
BPLER Heat Shock Rep1
|
BPLER cells
|
cell line: BPLER
treatment: 1H 42C heat shock
|
Gene expression data from BPLER cells after a 1H 42C heat shock
|
| Sample_geo_accession | GSM937107
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937107/suppl/GSM937107_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B11_440262.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
GSM937108 | GPL3921 |
|
BPLER Heat Shock Rep2
|
BPLER cells
|
cell line: BPLER
treatment: 1H 42C heat shock
|
Gene expression data from BPLER cells after a 1H 42C heat shock
|
| Sample_geo_accession | GSM937108
| | Sample_status | Public on Aug 07 2012
| | Sample_submission_date | May 24 2012
| | Sample_last_update_date | Mar 18 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | In vitro cultured according to published conditions
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix standard instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Marc,,Mendillo
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM937nnn/GSM937108/suppl/GSM937108_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_B12_440260.CEL.gz
| | Sample_series_id | GSE38232
| | Sample_series_id | GSE38912
| | Sample_data_row_count | 22277
| | |
|
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