|
| Status |
Public on Jun 28, 2011 |
| Title |
Gastric cancer tissue samples (FFPE)_UK 6 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Gastric cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Gastric cancer
gender: male
race: UK patient
msi status: MSS
|
| 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 |
female reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: reference: 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. 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 |
|
