Search results for the GEO ID: GSE15053  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM375869 | GPL1261 |
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EB6
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ES cell
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treatment: ES cell control
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ES cell differentiated into Embryonal body
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| Sample_geo_accession | GSM375869
| | Sample_status | Public on Mar 18 2009
| | Sample_submission_date | Mar 02 2009
| | Sample_last_update_date | Mar 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
| | Sample_data_processing | Affymetrix GCOS was used with target intensity=100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hideo,,Ema
| | Sample_contact_email | hema@ims.u-tokyo.ac.jp
| | Sample_contact_department | The Institute of Medical Science
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 4-6-1 Shirokanedai, Minato-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 108-8639
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375869/suppl/GSM375869.CEL.gz
| | Sample_series_id | GSE15053
| | Sample_data_row_count | 45101
| | |
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GSM375870 | GPL1261 |
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ES_HoxB4_off
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ES cell
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treatment: HoxB4 off
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co-culture with OP9 cells in the absence of HOXB4
|
| Sample_geo_accession | GSM375870
| | Sample_status | Public on Mar 18 2009
| | Sample_submission_date | Mar 02 2009
| | Sample_last_update_date | Mar 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
| | Sample_data_processing | Affymetrix GCOS was used with target intensity=100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hideo,,Ema
| | Sample_contact_email | hema@ims.u-tokyo.ac.jp
| | Sample_contact_department | The Institute of Medical Science
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 4-6-1 Shirokanedai, Minato-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 108-8639
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375870/suppl/GSM375870.CEL.gz
| | Sample_series_id | GSE15053
| | Sample_data_row_count | 45101
| | |
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GSM375871 | GPL1261 |
|
ES_HoxB4_on
|
ES cell
|
treatment: HoxB4 on
|
co-culture with OP9 cells in the presence of HOXB4
|
| Sample_geo_accession | GSM375871
| | Sample_status | Public on Mar 18 2009
| | Sample_submission_date | Mar 02 2009
| | Sample_last_update_date | Mar 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
| | Sample_data_processing | Affymetrix GCOS was used with target intensity=100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hideo,,Ema
| | Sample_contact_email | hema@ims.u-tokyo.ac.jp
| | Sample_contact_department | The Institute of Medical Science
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 4-6-1 Shirokanedai, Minato-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 108-8639
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375871/suppl/GSM375871.CEL.gz
| | Sample_series_id | GSE15053
| | Sample_data_row_count | 45101
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