Search results for the GEO ID: GSE31280  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM775291 | GPL1261 |
|
EtOH, RARaKO, set 2
|
F9 RARaKO treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: RARaKO
cell line: F9
|
Set2
Gene expression data from EtOH treated RARaKO cells
|
| Sample_geo_accession | GSM775291
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775291/suppl/GSM775291_2AC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775292 | GPL1261 |
|
atRA RARaKO, set 2
|
F9 RARaKO treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: RARaKO
cell line: F9
|
Set2
Gene expression data from atRA treated RARaKO cells
|
| Sample_geo_accession | GSM775292
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775292/suppl/GSM775292_2ARC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775293 | GPL1261 |
|
EtOH, WT, set 2
|
F9 WT treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: WT
cell line: F9
|
Set2
Gene expression data from EtOH treated WT cells
|
| Sample_geo_accession | GSM775293
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775293/suppl/GSM775293_2WC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775294 | GPL1261 |
|
atRA WT, set 2
|
F9 WT treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: WT
cell line: F9
|
Set2
Gene expression data from atRA treated WT cells
|
| Sample_geo_accession | GSM775294
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775294/suppl/GSM775294_2WRC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775295 | GPL1261 |
|
EtOH, RARaKO, set 3
|
F9 RARaKO treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: RARaKO
cell line: F9
|
Set3
Gene expression data from EtOH treated RARaKO cells
|
| Sample_geo_accession | GSM775295
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775295/suppl/GSM775295_3AC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775296 | GPL1261 |
|
atRA RARaKO, set 3
|
F9 RARaKO treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: RARaKO
cell line: F9
|
Set3
Gene expression data from atRA treated RARaKO cells
|
| Sample_geo_accession | GSM775296
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775296/suppl/GSM775296_3ARC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775297 | GPL1261 |
|
EtOH, WT, set 3
|
F9 WT treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: WT
cell line: F9
|
Set3
Gene expression data from EtOH treated WT cells
|
| Sample_geo_accession | GSM775297
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775297/suppl/GSM775297_3WC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775298 | GPL1261 |
|
atRA WT, set 3
|
F9 WT treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: WT
cell line: F9
|
Set3
Gene expression data from atRA treated WT cells
|
| Sample_geo_accession | GSM775298
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775298/suppl/GSM775298_3WRC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775299 | GPL1261 |
|
EtOH, RARaKO, set 4
|
F9 RARaKO treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: RARaKO
cell line: F9
|
Set4
Gene expression data from EtOH treated RARaKO cells
|
| Sample_geo_accession | GSM775299
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775299/suppl/GSM775299_4AC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775300 | GPL1261 |
|
atRA RARaKO, set 4
|
F9 RARaKO treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: RARaKO
cell line: F9
|
Set4
Gene expression data from atRA treated RARaKO cells
|
| Sample_geo_accession | GSM775300
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775300/suppl/GSM775300_4ARC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775301 | GPL1261 |
|
EtOH, WT, set 4
|
F9 WT treated 8hr with EtOH
|
treatment: EtOH + cycloheximide
genotype: WT
cell line: F9
|
Set4
Gene expression data from EtOH treated WT cells
|
| Sample_geo_accession | GSM775301
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775301/suppl/GSM775301_4WC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
GSM775302 | GPL1261 |
|
atRA WT, set 4
|
F9 WT treated 8hr with atRA
|
treatment: atRA + cycloheximide
genotype: WT
cell line: F9
|
Set4
Gene expression data from atRA treated WT cells
|
| Sample_geo_accession | GSM775302
| | Sample_status | Public on Aug 10 2011
| | Sample_submission_date | Aug 09 2011
| | Sample_last_update_date | Aug 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
| | Sample_growth_protocol_ch1 | F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
| | 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 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000-7G.
| | Sample_data_processing | The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kristian,Bruun,Laursen
| | Sample_contact_email | krl2004@med.cornell.edu
| | Sample_contact_laboratory | Lorraine Gudas
| | Sample_contact_department | Pharmacology
| | Sample_contact_institute | Weill Cornell Medical College
| | Sample_contact_address | 1300 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_zip/postal_code | NY 10065
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM775nnn/GSM775302/suppl/GSM775302_4WRC.cel.gz
| | Sample_series_id | GSE31280
| | Sample_data_row_count | 37661
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
