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Sample GSM197699 Query DataSets for GSM197699
Status Public on Oct 15, 2008
Title Adenoma 1 (F38A1_s68_b16)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics Adenoma 1
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 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 n/a
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 Oct 15, 2008
Contact name Daoud Sie
E-mail(s) [email protected]
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 (1)
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

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 5165.5 204 8831 134 -0.81 0
2 5370 201 8644 133 -0.72 0
3 5521.5 209 8849 135 -0.71 0
4 7780 199 11907.5 136 -0.63 0 -0.0148 -0.0148
5 7929 202 11667 137 -0.58 0 -0.0148 -0.0148
6 7931.5 197 12187 136 -0.64 0 -0.0148 -0.0148
7 6753 193 11130 133 -0.75 0
8 6700 190 11053 134 -0.75 0
9 6599.5 185 11277 135 -0.8 0
10 4120 178 6694 133 -0.73 0 -0.0419 -0.0419
11 4066 183 7099 134 -0.84 0 -0.0419 -0.0419
12 4109 176 6913 130 -0.79 0 -0.0419 -0.0419
13 7426 178 12963 128 -0.82 0
14 7683 178 13341.5 131 -0.82 0
15 7675 171 13373 134 -0.82 0
16 5191 175 8606.5 134 -0.76 0 -0.0419 -0.0419
17 5094 178 8321 135 -0.74 0 -0.0419 -0.0419
18 5122.5 172 8403.5 134 -0.74 0 -0.0419 -0.0419
19 5859.5 215 9763.5 135 -0.77 0
20 5754 212 9499 135.5 -0.76 0

Total number of rows: 15528

Table truncated, full table size 676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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