Result

Search results for the GEO ID: GSE14526

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM363583

GPL570

HCT116_aza0_tsa0

Colon cancer cell line

cell line: HCT116

No treatment with 5-aza-2-deoxycytidine and trichostatin A

Sample_geo_accession	GSM363583
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jan 23 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM363nnn/GSM363583/suppl/GSM363583_HCT116_aza0_tsa0.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM363584

GPL570

HCT116_aza3_tsa0

Colon cancer cell line

cell line: HCT116

Treated with 3uM 5-aza-2-deoxycytidine and no trichostatin A

Sample_geo_accession	GSM363584
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jan 23 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM363nnn/GSM363584/suppl/GSM363584_HCT116_aza3_tsa0.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM363585

GPL570

HCT116_aza3_tsa300

Colon cancer cell line

cell line: HCT116

Treated with 3uM 5-aza-2-deoxycytidine and 300 nM trichostatin A

Sample_geo_accession	GSM363585
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jan 23 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM363nnn/GSM363585/suppl/GSM363585_HCT116_aza3_tsa300.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM363586

GPL570

NormalColon

normal colon

tissue: adult normal colon

Ambion, cat#7986, lot#071P10B

Sample_geo_accession	GSM363586
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jan 23 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM363nnn/GSM363586/suppl/GSM363586.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM363587

GPL570

FetalColon

fetal colon

tissue: fetal colon

Stratagene, cat#738009, lot#0610532

Sample_geo_accession	GSM363587
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jan 23 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM363nnn/GSM363587/suppl/GSM363587.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM427057

GPL570

SW480_aza0_tsa0

Colon cancer cell line

cell line: SW480

No treatment with 5-aza-2-deoxycytidine and trichostatin A

Sample_geo_accession	GSM427057
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jul 13 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM427nnn/GSM427057/suppl/GSM427057.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM427058

GPL570

SW480_aza3_tsa0

Colon cancer cell line

cell line: SW480

Treated with 3uM 5-aza-2-deoxycytidine and no trichostatin A

Sample_geo_accession	GSM427058
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jul 13 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM427nnn/GSM427058/suppl/GSM427058.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

GSM427059

GPL570

SW480_aza3_tsa300

Colon cancer cell line

cell line: SW480

Treated with 3uM 5-aza-2-deoxycytidine and 300 nM trichostatin A

Sample_geo_accession	GSM427059
Sample_status	Public on Jan 05 2010
Sample_submission_date	Jul 13 2009
Sample_last_update_date	Jan 05 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 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	GPL570
Sample_contact_name	Atsushi,,Kaneda
Sample_contact_email	kaneda@genome.rcast.u-tokyo.ac.jp
Sample_contact_laboratory	Genome Science Division
Sample_contact_department	RCAST
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1 Komaba
Sample_contact_city	Meguro-ku
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/GSM427nnn/GSM427059/suppl/GSM427059.CEL.gz
Sample_series_id	GSE14526
Sample_data_row_count	54675

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