Search results for the GEO ID: GSE30985 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM767889 | GPL570 |
|
DMSO_rep_1
|
HCT116 cells were treated for 72 hours with DMSO
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with DMSO
|
Sample_geo_accession | GSM767889
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767889/suppl/GSM767889.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767890 | GPL570 |
|
DMSO_rep_2
|
HCT116 cells were treated for 72 hours with DMSO
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with DMSO
|
Sample_geo_accession | GSM767890
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767890/suppl/GSM767890.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767891 | GPL570 |
|
DMSO_rep_3
|
HCT116 cells were treated for 72 hours with DMSO
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with DMSO
|
Sample_geo_accession | GSM767891
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767891/suppl/GSM767891.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767892 | GPL570 |
|
DMSO_rep_4
|
HCT116 cells were treated for 72 hours with DMSO
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with DMSO
|
Sample_geo_accession | GSM767892
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767892/suppl/GSM767892.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767893 | GPL570 |
|
DAC_5uM_rep1
|
HCT116 cells were treated for 72 hours with Decitabine (5uM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (5uM)
|
Sample_geo_accession | GSM767893
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767893/suppl/GSM767893.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767894 | GPL570 |
|
DAC_5uM_rep2
|
HCT116 cells were treated for 72 hours with Decitabine (5uM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (5uM)
|
Sample_geo_accession | GSM767894
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767894/suppl/GSM767894.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767895 | GPL570 |
|
DAC_120nM_rep1
|
HCT116 cells were treated for 72 hours with Decitabine (120nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (120nM)
|
Sample_geo_accession | GSM767895
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767895/suppl/GSM767895.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767896 | GPL570 |
|
DAC_120nM_rep2
|
HCT116 cells were treated for 72 hours with Decitabine (120nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (120nM)
|
Sample_geo_accession | GSM767896
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767896/suppl/GSM767896.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767897 | GPL570 |
|
phos_G669071_63uM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)
|
Sample_geo_accession | GSM767897
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767897/suppl/GSM767897.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767898 | GPL570 |
|
phos_G669071_63uM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)
|
Sample_geo_accession | GSM767898
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767898/suppl/GSM767898.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767899 | GPL570 |
|
phos_G669071_6uM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)
|
Sample_geo_accession | GSM767899
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767899/suppl/GSM767899.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767900 | GPL570 |
|
phos_G669071_6uM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)
|
Sample_geo_accession | GSM767900
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767900/suppl/GSM767900.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767901 | GPL570 |
|
ester_G668684_7uM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)
|
Sample_geo_accession | GSM767901
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767901/suppl/GSM767901.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767902 | GPL570 |
|
ester_G668684_7uM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)
|
Sample_geo_accession | GSM767902
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767902/suppl/GSM767902.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767903 | GPL570 |
|
ester_G668684_150nM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)
|
Sample_geo_accession | GSM767903
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767903/suppl/GSM767903.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767904 | GPL570 |
|
ester_G668684_150nM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)
|
Sample_geo_accession | GSM767904
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767904/suppl/GSM767904.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767905 | GPL570 |
|
Aza_1500nM_rep1
|
HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)
|
Sample_geo_accession | GSM767905
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767905/suppl/GSM767905.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767906 | GPL570 |
|
Aza_1500nM_rep2
|
HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)
|
Sample_geo_accession | GSM767906
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767906/suppl/GSM767906.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767907 | GPL570 |
|
Aza_150nM_rep1
|
HCT116 cells were treated for 72 hours with Azacytidine(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(150 nM)
|
Sample_geo_accession | GSM767907
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767907/suppl/GSM767907.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767908 | GPL570 |
|
Aza_150nM_rep2
|
HCT116 cells were treated for 72 hours with Azacytidine(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(150 nM)
|
Sample_geo_accession | GSM767908
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767908/suppl/GSM767908.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767909 | GPL570 |
|
Aza_G669043_1500nM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)
|
Sample_geo_accession | GSM767909
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767909/suppl/GSM767909.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767910 | GPL570 |
|
Aza_G669043_1500nM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)
|
Sample_geo_accession | GSM767910
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767910/suppl/GSM767910.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767911 | GPL570 |
|
Aza_G669043_150nM_rep1
|
HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)
|
Sample_geo_accession | GSM767911
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767911/suppl/GSM767911.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
GSM767912 | GPL570 |
|
Aza_G669043_150nM_rep2
|
HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)
|
cell line: HCT-116
|
Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)
|
Sample_geo_accession | GSM767912
| Sample_status | Public on Dec 01 2011
| Sample_submission_date | Jul 27 2011
| Sample_last_update_date | Dec 01 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.
| Sample_growth_protocol_ch1 | HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.
| Sample_hyb_protocol | The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G
| Sample_data_processing | Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.
| Sample_platform_id | GPL570
| Sample_contact_name | Paul,,Mason
| Sample_contact_email | paul.mason@genzyme.com
| Sample_contact_institute | Genzyme Corporation
| Sample_contact_address | 153 Second Ave
| Sample_contact_city | Waltham
| Sample_contact_zip/postal_code | 02451
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM767nnn/GSM767912/suppl/GSM767912.CEL.gz
| Sample_series_id | GSE30985
| Sample_data_row_count | 54675
| |
|
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