Search results for the GEO ID: GSE18973  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM446264 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown1_rep1
|
HNF4a&HNF4g_knockdown1
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn1_try1
|
| Sample_geo_accession | GSM446264
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446264/suppl/GSM446264.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446265 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown2_rep1
|
HNF4a&HNF4g_knockdown2
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn2_try1
|
| Sample_geo_accession | GSM446265
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446265/suppl/GSM446265.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446266 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown_control_rep1
|
HNF4a&HNF4g_knockdown_control
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwncontrol_try1
|
| Sample_geo_accession | GSM446266
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446266/suppl/GSM446266.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446268 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown1_rep2
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HNF4a&HNF4g_knockdown1
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cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn1_try2
|
| Sample_geo_accession | GSM446268
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446268/suppl/GSM446268.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446269 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown2_rep2
|
HNF4a&HNF4g_knockdown2
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn2_try2
|
| Sample_geo_accession | GSM446269
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446269/suppl/GSM446269.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446270 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown_control_rep2
|
HNF4a&HNF4g_knockdown_control
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwncontrol_try2
|
| Sample_geo_accession | GSM446270
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446270/suppl/GSM446270.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446271 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown1_rep3
|
HNF4a&HNF4g_knockdown1
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn1_try3
|
| Sample_geo_accession | GSM446271
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446271/suppl/GSM446271.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446272 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown2_rep3
|
HNF4a&HNF4g_knockdown2
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwn2_try3
|
| Sample_geo_accession | GSM446272
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446272/suppl/GSM446272.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
| | |
|
GSM446273 | GPL570 |
|
HepG2_HNF4a&HNF4g_knockdown_control_rep3
|
HNF4a&HNF4g_knockdown_control
|
cell line: HepG2
cell type: hepatocellular carcinoma
|
HepG2_HNF4a&HNF4gknockdouwncontrol_try3
|
| Sample_geo_accession | GSM446273
| | Sample_status | Public on Dec 22 2010
| | Sample_submission_date | Aug 28 2009
| | Sample_last_update_date | Dec 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 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 Microarray Suite v5.0 with target intensity=100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kenji,,Daigo
| | Sample_contact_email | daigo@lsbm.org
| | Sample_contact_phone | +81-3-5452-5236
| | Sample_contact_fax | +81-3-5452-5236
| | Sample_contact_laboratory | Departments of Molecular Biology and Medicine
| | Sample_contact_department | Research Center for Advanced Science and Technology
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | #35 4-6-1 Komaba
| | Sample_contact_city | Meguro
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 153-8904
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM446nnn/GSM446273/suppl/GSM446273.CEL.gz
| | Sample_series_id | GSE18973
| | Sample_series_id | GSE18990
| | Sample_data_row_count | 54675
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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