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Sample GSM800767 Query DataSets for GSM800767
Status Public on Mar 20, 2012
Title patient 033b, cancer, homogenized
Sample type RNA
 
Source name surgically resected material
Organism Homo sapiens
Characteristics metastasis: none
Stage: 2a
tissue: cancer, homogenized
Treatment protocol Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were used. Five cell lines were treated with 5-aza-2'-deoxycytidine.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
Label biotin
Label protocol cRNA was prepared using one-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
Description Gene expression profile of surgically resected material
Data processing The data was normalized by robust multichip analysis (RMA) using Gene Expression Console (Affymetrix)
 
Submission date Sep 22, 2011
Last update date Mar 20, 2012
Contact name Kaoru Mogushi
E-mail(s) [email protected]
Phone +81-3-5802-1797
Organization name Juntendo University
Department Intractable Disease Research Center
Street address 2-1-1 Hongo
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-8421
Country Japan
 
Platform ID GPL570
Series (1)
GSE32323 Screening for Epigenetically Masked Genes in Colorectal Cancer using 5-aza-2’-deoxycytidine treatment, Microarray and Gene Expression Profile
Relations
Reanalysis of GSM452654

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 7.392206
AFFX-BioB-M_at 7.713408
AFFX-BioB-3_at 7.276075
AFFX-BioC-5_at 8.576728
AFFX-BioC-3_at 8.958097
AFFX-BioDn-5_at 10.30274
AFFX-BioDn-3_at 11.60519
AFFX-CreX-5_at 12.44761
AFFX-CreX-3_at 13.05877
AFFX-DapX-5_at 6.632053
AFFX-DapX-M_at 10.69562
AFFX-DapX-3_at 11.688
AFFX-LysX-5_at 5.608195
AFFX-LysX-M_at 8.497992
AFFX-LysX-3_at 9.669805
AFFX-PheX-5_at 6.469542
AFFX-PheX-M_at 8.853856
AFFX-PheX-3_at 9.638125
AFFX-ThrX-5_at 5.321977
AFFX-ThrX-M_at 7.826028

Total number of rows: 54675

Table truncated, full table size 1052 Kbytes.




Supplementary file Size Download File type/resource
GSM800767_chip_array_C33T-H.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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