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Sample GSM574282 Query DataSets for GSM574282
Status Public on Jun 13, 2011
Title Gastric cancer tissue samples (FFPE) 19_control
Sample type genomic
 
Channel 1
Source name Gastric cancer
Organism Homo sapiens
Characteristics tissue: Gastric cancer
site: control
tumor site: control
tnm: control
age: control
gender: control
platform_id type: oligo
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 female reference DNA
Organism Homo sapiens
Characteristics tissue: Pooled DNA from the blood of 18 normal female 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) [email protected]
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 GPL2827
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
1 -0.95242845
2 -0.99087199
3 -1.227908693
4 -0.71713623
5 -0.581880215
6 -0.569391254
7 -1.373154371
8 -0.779947454
9 -1.366702309
10 -1.122933138
11 -1.634729846
12 -1.079198352
13 -1.511238636
14 -1.577229648
15 -1.081812032
16 -1.505192971
17 -0.643001179
18 -0.59276451
19 -1.426113219
20 -1.261434112

Total number of rows: 25905

Table truncated, full table size 403 Kbytes.




Supplementary file Size Download File type/resource
GSM574282_GC19_control.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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