NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM710561 Query DataSets for GSM710561
Status Public on Feb 17, 2012
Title HumanTumor_FreshFrozen_CRC034
Sample type RNA
 
Source name human tumor, colon primary, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: Colon
metastatic tumor site: Colon
Extracted molecule total RNA
Extraction protocol Tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
Scan protocol GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
Data processing The gene expression data were RMA-estimated using the R statistical platform with the Bioconductor affymetrix package.
 
Submission date Apr 18, 2011
Last update date May 14, 2012
Contact name David Hsu
E-mail(s) hsu00018@dm.duke.edu
Phone 919-684-1739
Fax 919-668-4777
Organization name Duke University
Department Institute for Genome Sciences and Policy
Street address Rm 2167 CIEMAS Bldg, 101 Science Dr.
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL571
Series (1)
GSE28691 Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal Cancer

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA signal

Data table
ID_REF VALUE
1007_s_at 9.866017942
1053_at 7.384758596
117_at 5.20491279
121_at 7.777401176
1255_g_at 3.528106833
1294_at 6.781441207
1316_at 5.072971106
1320_at 4.862830036
1405_i_at 5.322394533
1431_at 3.699067109
1438_at 6.627584537
1487_at 8.45495047
1494_f_at 5.091205035
1598_g_at 8.480167376
160020_at 6.789105346
1729_at 7.508811788
177_at 5.45771681
1773_at 5.709784681
179_at 8.25694937
1861_at 6.397014196

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM710561.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap