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Sample GSM197890 Query DataSets for GSM197890
Status Public on Oct 15, 2008
Title Carcinoma component of a progressed adenoma (P9C_s21_b16)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma component of a progressed adenoma
site: Colorectum
tumor site: Right colon
tnm: pT3N0M0
age: 62
gender: M
platform_id type: bac
Extracted molecule genomic DNA
Extraction protocol as described in Weiss et al, Mol Pathol. 1999 Oct;52(5):243-51.
Label Cy3
Label protocol as described by Snijders et al, Nat Genetics, volume 29, p 263-4
 
Channel 2
Source name female Reference DNA
Organism Homo sapiens
Characteristics sample type: A pool of ten normal individuals
Extracted molecule genomic DNA
Extraction protocol DNAzol (Invitrogen) according to manufacturer's protocol
Label Cy5
Label protocol as described by Snijders et al, Nat Genetics, volume 29, p 263-4
 
 
Hybridization protocol as described by Carvalho et al, Cell Oncol. 2006;28(5-6):283-94.
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description CRC19
Data processing Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the July 2003 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.
 
Submission date Jun 05, 2007
Last update date Aug 09, 2010
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 GPL3442
Series (2)
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

Data table header descriptions
ID_REF
Signal Median CH1 spot signal channel 1 (Cy3)
Background Median CH1 background signal of channel 1 (Cy3)
Signal Median CH2 spot signal channel 2 (Cy5)
Background Median CH2 background signal of channel 1 (Cy5)
Log2ratio
Flag A flag to highlight spots that suffer from poor printing and other experimental artefacts (0 acceptable; 1-4 not acceptable)
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Normalized value of the log2ratio. Flagged features are excluded. Values where also deleted if the each triplicate had a Standard Deviation higher than 0.2.

Data table
ID_REF Signal Median CH1 Background Median CH1 Signal Median CH2 Background Median CH2 Log2ratio Flag VALUE UNF_VALUE
1 11489 114 15714 199.5 -0.45 0
2 10870.5 78 15628.5 215 -0.51 0
3 11441.5 57 16234 145 -0.5 0
4 15355.5 63.5 19119.5 163.5 -0.31 0 0.0872 0.0872
5 15490 164 19295 193 -0.32 0 0.0872 0.0872
6 15551 84 19387.5 164 -0.31 0 0.0872 0.0872
7 11129 67 15927 133 -0.51 0
8 10672 106 16145 126.5 -0.6 0
9 10038.5 87 15125.5 110 -0.59 0
10 6953 113.5 8494 151.5 -0.29 0 0.0565 0.0565
11 6411 112.5 7946 124 -0.31 0 0.0565 0.0565
12 6413 84 8026 141 -0.32 0 0.0565 0.0565
13 9476 126.5 13750.5 150.5 -0.54 0
14 9026 111 13801 114 -0.62 0
15 9475 99.5 14174.5 140 -0.58 0
16 8627.5 38.5 10322 120.5 -0.25 0 0.1438 0.1438
17 8361 142 10203 156 -0.29 0 0.1438 0.1438
18 8444 95 10068.5 122.5 -0.25 0 0.1438 0.1438
19 9082 123 13373 153 -0.56 0
20 8335 123 12496 153 -0.59 0

Total number of rows: 15528

Table truncated, full table size 704 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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