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Sample GSM574260 Query DataSets for GSM574260
Status Public on Jun 13, 2011
Title Gastric cancer tissue samples (FFPE) 8
Sample type genomic
 
Channel 1
Source name Gastric cancer
Organism Homo sapiens
Characteristics tissue: Gastric cancer
site: Stomach
tumor site: Cardia
tnm: pT2N0M0
age: 71
gender: M
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 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) 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 GPL2842
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
13 -1.267506606
25 -0.817817892
28 -1.21431245
37 -1.065307621
46 -0.840701838
82 -1.325959987
88 -1.0309388
94 -1.638077148
97 -1.396567636
100 -1.441766316
106 -1.604067045
109 -2.161816955
112 -1.584812497
118 -1.364168313
121 -1.239060132
124 -1.110733765
127 -1.282967508
130 -1.484909307
139 -0.365071029
145 -1.413341775

Total number of rows: 2640

Table truncated, full table size 46 Kbytes.




Supplementary file Size Download File type/resource
GSM574260_GC8.txt.gz 1.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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