Search results for the GEO ID: GSE32288  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM799886 | GPL1261 |
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Yaf2wt_(OHT+) rep1
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Yaf2wt_(OHT+)
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strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: wild type, Rybp-depleted
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RYBP KO
Gene expression data from clone#3031+ (tamoxifen treated, Wild type of Yaf2 and Mut RYBP)
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| Sample_geo_accession | GSM799886
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799886/suppl/GSM799886_RMXXST096002.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
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GSM799887 | GPL1261 |
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Yaf2wt_(OHT-) rep1
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Yaf2wt_(OHT-)
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strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: wild type
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Wild tyep
Gene expression data from clone#3031- (nontreated, Wild type of Yaf2 and Wild type RYBP for control)
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| Sample_geo_accession | GSM799887
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799887/suppl/GSM799887_RMXXST097001.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
| | |
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GSM799888 | GPL1261 |
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Yaf2kd_(OHT+) rep1
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Yaf2kd_(OHT+)
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strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: yaf2 mutant, Rybp-depleted
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Yaf2 KD RYBP KO (I)
Gene expression data from clone#3086+ (tamoxifen treated, Mut Yaf2 and Mut RYBP), biological duplicate 1
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| Sample_geo_accession | GSM799888
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799888/suppl/GSM799888_RMXXST098001.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
| | |
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GSM799889 | GPL1261 |
|
Yaf2kd_(OHT-) rep1
|
Yaf2kd_(OHT-)
|
strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: yaf2 mutant
|
Yaf2 KD (I)
Gene expression data from clone#3086- (nontreated, Mut Yaf2 and wild type RYBP), biological duplicate 1
|
| Sample_geo_accession | GSM799889
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799889/suppl/GSM799889_RMXXST099001.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
| | |
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GSM799890 | GPL1261 |
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Yaf2kd_(OHT+) rep2
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Yaf2kd_(OHT+)
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strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: yaf2 mutant, Rybp-depleted
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Yaf2 KD RYBP KO (II)
Gene expression data from clone#3087+ (tamoxifen treated, Mut Yaf2 and Mut RYBP), biological duplicate 2
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| Sample_geo_accession | GSM799890
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799890/suppl/GSM799890_RMXXST100001.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
| | |
|
GSM799891 | GPL1261 |
|
Yaf2kd_(OHT-) rep2
|
Yaf2kd_(OHT-)
|
strain background: 129/B6 hybrid
cell type: embryonic stem cells
genotype/variation: yaf2 mutant
|
Yaf2 KD (II)
Gene expression data from clone#3087- (nontreated, Mut Yaf2 and wild type RYBP), biological duplicate 2
|
| Sample_geo_accession | GSM799891
| | Sample_status | Public on Apr 04 2012
| | Sample_submission_date | Sep 21 2011
| | Sample_last_update_date | Apr 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cell were treated with 0.8 µM of 4-hydroxytamoxifen for 24 hours to deplete Rybp.
| | Sample_growth_protocol_ch1 | ES cells were cultivated in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol following manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.
| | Sample_hyb_protocol | Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.
| | Sample_scan_protocol | GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.
| | Sample_data_processing | The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Takaho,A.,Endo
| | Sample_contact_email | takaho.endo@riken.jp
| | Sample_contact_laboratory | Laboratory for Integrative Genomics
| | Sample_contact_department | IMS
| | Sample_contact_institute | RIKEN
| | Sample_contact_address | 1-7-22 Suehiro, Tsurumi
| | Sample_contact_city | Yokohama
| | Sample_contact_state | Kanagawa
| | Sample_contact_zip/postal_code | 230-0045
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM799nnn/GSM799891/suppl/GSM799891_RMXXST102001.CEL.gz
| | Sample_series_id | GSE32288
| | Sample_series_id | GSE32294
| | Sample_data_row_count | 45101
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