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Sample GSM291388 Query DataSets for GSM291388
Status Public on Feb 20, 2009
Title CIN lesion grade 2/3 VUMC_HGCIN29_b45_s56
Sample type genomic
 
Channel 1
Source name uterine cervix
Organism Homo sapiens
Characteristics cervical intraepithelial neoplasia (CIN) lesion, grade 2/3
Extracted molecule genomic DNA
Extraction protocol as described in Van zeeburg et al, Cancer Res, volume 65, p 1271-76, 2005
Label Cy3
Label protocol as described by Snijders et al, Nat Genetics, volume 29, p 263-4
 
Channel 2
Source name Reference DNA
Organism Homo sapiens
Characteristics Pooled DNA from the blood of 10 normal male individuals
Extracted molecule genomic DNA
Extraction protocol as described in Wilting et al, J Pathol, volume 209, p 220-30
Label Cy5
Label protocol as ch1, Cy5 in stead of Cy3
 
 
Hybridization protocol Hybridisations were performed as described by Snijders et al, Nat Genetics, volume 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 – Perkin Elmer Life Sciences).
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description CIN2 lesion, patient age 25 years, contains high risk Human Papilloma Virus
Data processing Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 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 May 28, 2008
Last update date Feb 20, 2009
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 GPL2843
Series (1)
GSE11573 Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas

Data table header descriptions
ID_REF
Signal Median CH1 Spot signal in channel 1 (Cy3)
Background Median CH1 Background signal channel 1 (Cy3)
Signal Median CH2 Spot signal in channel 2 (Cy5)
Background Median CH2 Background signal channel 2 (Cy5)
Flag A flag to highlight spots that suffer from poor printing and other experimental artefacts (0 acceptable; 1-4 not acceptable)
Coriell BAC clones misbehaving in hybridisations with Coriell cell lines were flagged (0 acceptable; 1 not acceptable)
VALUE Normalized log2 ratio of the test (Cy3)/ reference (Cy5) sample

Data table
ID_REF Signal Median CH1 Background Median CH1 Signal Median CH2 Background Median CH2 Flag Coriell VALUE
1 636 344.5 1179 275 0 0
2 641 331 1112 262 0 0
3 625 324 1415 284 0 0
4 576 331 1999.5 405.5 3
5 611 338 1757 453 3
6 610 336.5 2044 465 3
7 5060 318 23888.5 299.5 0 0 -0.079877968
8 5044 309 22062 281.5 0 0 -0.079877968
9 4924 308.5 22889 262 0 0 -0.079877968
10 376 316 428 227.5 0
11 377 313 434 225 0
12 395 315 432.5 224 0
13 908 316 2807.5 230 0 0
14 1274 318 3310.5 235 0 0
15 835 328 2570 253 0 0
16 390.5 325 395 239 0
17 395 319 408.5 236 0
18 420 308 441.5 233 0
19 1905 308 7987 237 0 0 -0.03732606
20 2153 316.5 7634 248.5 3 0 -0.03732606

Total number of rows: 19200

Table truncated, full table size 723 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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