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Sample GSM574279 Query DataSets for GSM574279
Status Public on Jun 13, 2011
Title Gastric cancer tissue samples (FFPE) 27
Sample type genomic
 
Channel 1
Source name Gastric cancer
Organism Homo sapiens
Characteristics tissue: Gastric cancer
site: Stomach
tumor site: Cardia
tnm: pT2N0M0
age: 54
gender: F
platform_id type: bac
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
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: 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
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 Aug 04, 2010
Last update date Jun 13, 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 GPL2843
Series (1)
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5) representing tumor/normal, if more than one spot per clone/probe median was taken.

Data table
ID_REF VALUE
25
28 -2.950664021
31
34 -3.644513612
37 -2.515250187
40 -2.790560837
43
46
52
55 -3.710662211
58
67 -3.461311589
70 -2.982068917
73 -3.18919864
76
79 -3.556923771
82 -3.422498913
85 -3.24915319
88 -3.186019144
91 -3.670421708

Total number of rows: 2747

Table truncated, full table size 44 Kbytes.




Supplementary file Size Download File type/resource
GSM574279_GC27.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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