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Sample GSM197662 Query DataSets for GSM197662
Status Public on Oct 15, 2008
Title Carcinoma (F12C_s42_b16)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma
site: Colorectum
tumor site: Left colon
tnm: pT3N0M0
age: 65
gender: M
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 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 CRC17
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 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 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 6551.5 157.5 7683.5 122 -0.24 0
2 7020 165 8110 124 -0.22 0
3 6724.5 159 7829 122 -0.23 0
4 8740 163 9970 121 -0.2 0 0.128 0.128
5 8709.5 162 10023 125 -0.21 0 0.128 0.128
6 8650 167 9967 128 -0.21 0 0.128 0.128
7 7141 166 8546 130 -0.27 0
8 7109.5 165 8471 133 -0.26 0
9 6946 163 8451.5 132 -0.29 0
10 3864 158 4611.5 125 -0.28 0 0.0472 0.0472
11 3785 152 4429 119 -0.25 0 0.0472 0.0472
12 3672 147 4264 117 -0.23 0 0.0472 0.0472
13 7127 146 8302 113 -0.23 0
14 7258 148 8396 114 -0.22 0
15 7200 148 8390 116 -0.23 0
16 5386 151 6169.5 116 -0.21 0 0.128 0.128
17 5135 151 5722 118 -0.17 0 0.128 0.128
18 5093 147 5750.5 118.5 -0.19 0 0.128 0.128
19 6447.5 160 7617 121 -0.25 0
20 6438 165 7699 123.5 -0.27 0

Total number of rows: 15528

Table truncated, full table size 668 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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