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Sample GSM620922 Query DataSets for GSM620922
Status Public on Nov 01, 2012
Title Colorectal cancer CRC05 [aCGH]
Sample type genomic
 
Channel 1
Source name colorectal carcinoma
Organism Homo sapiens
Characteristics gender: male
age: 68
crc location: Colon-Ca
ms status: microsatellite stable (MSS)
kras- and braf mutational status: KRAS-wt; BRAF-wt
Extracted molecule genomic DNA
Extraction protocol Colorectal cancer samples were collected from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation.
Human peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) or by magnetic bead separation from buffy coats of healthy donors using CD14 antibodies. DNA from monocytes was prepared using Qiagen Blood & Cell Culture DNA Kit. Leukapharesis was performed in agreement with the Institutional ethical review board of the University of Regensburg.
Label Cy 5–dUTP
Label protocol Genome-wide analysis of unbalanced chromosomal changes was done by microarray-based Comparative Genomic Hybridization (aCGH). CRC DNA (1 µg) as well as normal reference DNA (mixed normal human monocytes, 1 µg) were labelled using the Genomic DNA Enzymatic Labeling Kit (Agilent)
 
Channel 2
Source name normal monocyte
Organism Homo sapiens
Characteristics gender: male
sample: normal monocytes; mixture of six donors
Extracted molecule genomic DNA
Extraction protocol Colorectal cancer samples were collected from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation.
Human peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) or by magnetic bead separation from buffy coats of healthy donors using CD14 antibodies. DNA from monocytes was prepared using Qiagen Blood & Cell Culture DNA Kit. Leukapharesis was performed in agreement with the Institutional ethical review board of the University of Regensburg.
Label Cy 3–dUTP
Label protocol Genome-wide analysis of unbalanced chromosomal changes was done by microarray-based Comparative Genomic Hybridization (aCGH). CRC DNA (1 µg) as well as normal reference DNA (mixed normal human monocytes, 1 µg) were labelled using the Genomic DNA Enzymatic Labeling Kit (Agilent)
 
 
Hybridization protocol Labelled samples were hybridized on Human 4x180K CGH SurePrint G3 Microarrays (Agilent, GPL10123) according to the manufacturer’s instructions.
Scan protocol Images were scanned after washing using a DNA microarray scanner (Agilent)
Description Comparative genomic hybridization of CRC DNA samples against a common reference
Data processing Image data was processed using Feature Extraction Software 10 (Agilent) and analyzed using Agilent Genomic Workbench
 
Submission date Nov 09, 2010
Last update date Nov 01, 2012
Contact name Michael Rehli
E-mail(s) michael.rehli@klinik.uni-r.de
Organization name University Hospital Regensburg
Department Internal Med III
Street address F.-J.-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93042
Country Germany
 
Platform ID GPL10123
Series (2)
GSE25228 Chromosomal abnormalities in colorectal cancer
GSE25229 Genome-wide analysis of unbalanced chromosomal changes in colorectal carcinoma

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.379839648e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
14 0.000000000e+000
15 -9.640675582e-001
16 -8.068146473e-001
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4221 Kbytes.




Supplementary file Size Download File type/resource
GSM620922_CRC05_252206012403_200911111534_S01_CGH_105_Dec08_1_1.txt.gz 50.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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