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Sample GSM903629 Query DataSets for GSM903629
Status Public on Nov 14, 2014
Title Colorectal cancer tissue sample (FFPE) 323
Sample type genomic
 
Channel 1
Source name colorectal cancer, CAIRO2 arm A
Organism Homo sapiens
Characteristics tissue: colorectal cancer (FFPE)
study: CAIRO2
study arm: A
progression-free survival first line (days): 238
progression: yes
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).
Label Cy3
Label protocol DNA labeling protocol according to Enzo Life Sciences.
 
Channel 2
Source name normal colorectum mucosa
Organism Homo sapiens
Characteristics tissue: normal colon mucosa
patient: same patient as in ch1
sample type: reference
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).
Label Cy5
Label protocol DNA labeling protocol according to Enzo Life Sciences.
 
 
Hybridization protocol Hybridization protocol available via www.agilent.com.
Scan protocol Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.
Description CAIRO2 arm A: capecitabine, oxaliplatin and bevacizumab
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.
Data processing The profiles were dewaved (van de wiel et al., Bioinformatics. 2009 (PMID 19276148)), median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al., Bioinformatics. 2007 (PMID 17267432)).
 
Submission date Mar 27, 2012
Last update date Nov 14, 2014
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 GPL8687
Series (2)
GSE36864 Genomic landscape of metastatic colorectal cancer
GSE63216 Recurrent breakpoint genes in colorectal cancer

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy3/Cy5) representing tumor/normal

Data table
ID_REF VALUE
81584 0
115021 -0.24
59850 -0.25
123164 -0.07
140376 0.03
111805 0.16
91785 -0.25
55410 -0.23
49634 0.06
61425 -0.01
178535 -0.03
70828 -0.17
177952 0
122808 -0.52
64151 -0.48
60883 -0.1
129698 0
140610 0
180564 -0.19
37368 -0.01

Total number of rows: 173368

Table truncated, full table size 1986 Kbytes.




Supplementary file Size Download File type/resource
GSM903629_US22502676_252252210254_S01_CGH_105_Dec08_1_2.txt.gz 18.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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