|
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.
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|
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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 |
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