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Sample GSM197646 Query DataSets for GSM197646
Status Public on Oct 15, 2008
Title Carcinoma component of a progressed adenoma (P27C_s60_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: Rectum
tnm: pTxN0M0
age: 70
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 CRC12
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 6244 375 11706 213 -0.97 0 0.1577 0.1577
2 6028 383 10657.5 189 -0.89 0 0.1577 0.1577
3 6501 375 11346 185 -0.87 0 0.1577 0.1577
4 13567 358 27066.5 204 -1.02 0 0.0392 0.0392
5 13554 446 24871 197 -0.91 0 0.0392 0.0392
6 13481 424.5 26159 175 -0.99 0 0.0392 0.0392
7 3692 396 4003.5 175.5 -0.22 0
8 2044 385 5328.5 229 -1.62 3
9 3021 389 5491 172 -1.01 0
10 6243 392 13155 158 -1.15 0 -0.091 -0.091
11 6075.5 375.5 12134 168 -1.07 0 -0.091 -0.091
12 5999 392 12044 159.5 -1.08 0 -0.091 -0.091
13 1503 400 2877 198 -1.28 0
14 2324 410 2074 153 -0.01 0
15 2391 458.5 3900 180 -0.94 0
16 6409.5 416 12471 192.5 -1.03 0 0.0392 0.0392
17 6909.5 360 12873 186 -0.95 0 0.0392 0.0392
18 7175 338 13350 168 -0.95 0 0.0392 0.0392
19 2938 373 6767 162 -1.36 3 0.0082
20 6552 478 8571 191.5 -0.46 0 0.0082 0.0082

Total number of rows: 17328

Table truncated, full table size 746 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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