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Sample GSM197811 Query DataSets for GSM197811
Status Public on Oct 15, 2008
Title Carcinoma (F10C_s73_b21)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma
site: Colorectum
tumor site: Colon
tnm: pTxN2M0
age: 57
gender: F
platform_id type: bac
Extracted molecule genomic DNA
Extraction protocol protocol available on www.vumc.nl/microarrays
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 CRC10
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 frmo poor prinitng 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 10856 306 8019 187 0.43 0 0.2776 0.2776
2 11342.5 422 8360 213 0.42 0 0.2776 0.2776
3 11808 453 8839 229 0.4 0 0.2776 0.2776
4 20010 323 15858.5 233.5 0.33 0 -0.0396 -0.0396
5 20782 405 16032 199 0.36 0 -0.0396 -0.0396
6 21102.5 364.5 18937.5 227 0.15 0 -0.0396 -0.0396
7 6834 379 4918.5 205 0.45 0
8 5847 417 4853 211 0.23 0
9 6309.5 544 4001 190 0.6 0
10 8930 446 8482.5 203 0.04 0 -0.0396 -0.0396
11 9318 454 8689 190 0.06 0 -0.0396 -0.0396
12 8725.5 447 8195 231 0.06 0 -0.0396 -0.0396
13 1715.5 473 1852 199 -0.41 0 0.2175 0.2175
14 1848 425 2769 215.5 -0.84 0 0.2175 0.2175
15 1951.5 402 2720.5 199 -0.7 0 0.2175 0.2175
16 10328 393 10243 222 -0.01 0 -0.0396 -0.0396
17 10219 437 9395.5 189.5 0.09 0 -0.0396 -0.0396
18 9985 420 9691 228 0.02 0 -0.0396 -0.0396
19 8141 431 6830 187.5 0.22 0 0.2175 0.2175
20 10051 311 8406 209.5 0.25 0 0.2175 0.2175

Total number of rows: 17328

Table truncated, full table size 740 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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