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Sample GSM563476 Query DataSets for GSM563476
Status Public on Jun 28, 2011
Title Gastric cancer tissue samples (FFPE)_S 53
Sample type genomic
 
Channel 1
Source name Gastric cancer
Organism Homo sapiens
Characteristics tissue: Gastric cancer
gender: female
race: native SA patient
msi status: MSI-L
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51. DNA was isolated using commercially available DNA isolation kits (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands and QIAamp microkit; Qiagen, Hilden, Germany).
Label Cy3
Label protocol Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)
 
Channel 2
Source name male reference DNA
Organism Homo sapiens
Characteristics tissue: reference: Pooled DNA from the blood of 18 normal male individuals
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51. DNA was isolated using commercially available DNA isolation kits (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands and QIAamp microkit; Qiagen, Hilden, Germany).
Label Cy5
Label protocol Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)
 
 
Hybridization protocol As described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51
Scan protocol Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.
Description A pool of DNA from blood of normal individuals
Data processing Bluefuse software version 3.4 (BlueGnome, Cambridge, UK) was used for automatic feature extraction. Spots were excluded when the quality flag was below 1 or the confidence value was below 0.1. Log2 tumor to normal ratio was calculated for each clone and median block normalization was used to normalize the data.
 
Submission date Jul 07, 2010
Last update date Jun 28, 2011
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL7394
Series (1)
GSE22789 Gastric cancers of Western European and African patients

Data table header descriptions
ID_REF
VALUE normalized log2 ratio Cy3/Cy5 (tumor/normal)

Data table
ID_REF VALUE
10617 null
10768 null
10919 null
7085 -0.339
7236 -0.339
7387 -0.339
4942 null
5093 null
5244 null
13265 0.385
13416 0.385
13525 0.385
14588 1.216
14739 1.216
14848 1.216
18997 -0.24
19148 -0.24
19299 -0.24
10707 0.287
10816 0.287

Total number of rows: 21168

Table truncated, full table size 229 Kbytes.




Supplementary file Size Download File type/resource
GSM563476.txt.gz 401.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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