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Sample GSM197650 Query DataSets for GSM197650
Status Public on Oct 15, 2008
Title Carcinoma component of a progressed adenoma (P29C_s34_b21)
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: pTxN2Mx
age: 58
gender: F
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 male 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 CRC11
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 04, 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 GPL3443
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 2971 58 6549.5 47 -1.16 3 0.0645
2 4622.5 118.5 3944.5 70 0.22 0 0.0645 0.0645
3 6818 136 6544 45 0.04 0 0.0645 0.0645
4 13278 104 13250 27 -0.01 0 -0.0394 -0.0394
5 10864 101 13309 51 -0.3 0 -0.0394 -0.0394
6 13248.5 142 14068.5 45 -0.1 0 -0.0394 -0.0394
7 7140.5 128 7162 53 -0.02 3
8 6589.5 89 4596 10 0.5 0
9 6294.5 107 6222 34 0 0
10 4208 81 6554 32 -0.66 0 -0.0787 -0.0787
11 5154.5 85 6344 24 -0.32 0 -0.0787 -0.0787
12 4646 94 6224 21.5 -0.45 0 -0.0787 -0.0787
13 2214 83.5 2558 32 -0.25 1
14 3513 56 2894 3 0.26 1
15 656.5 82 602 22 -0.01 1
16 6117 128 7523 33 -0.32 0 -0.0394 -0.0394
17 4977.5 91 7848 36 -0.68 0 -0.0394 -0.0394
18 6400.5 111.5 7246 40.5 -0.2 0 -0.0394 -0.0394
19 7262 104.5 6282 18 0.19 0 0.0645 0.0645
20 7456 79 6648.5 37 0.16 0 0.0645 0.0645

Total number of rows: 17328

Table truncated, full table size 701 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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