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Sample GSM580073 Query DataSets for GSM580073
Status Public on Aug 02, 2011
Title Control 20 baseline Squamous Metaplasia
Sample type genomic
 
Channel 1
Source name Bronchial tissue, AFB-visualized
Organism Homo sapiens
Characteristics case number: Control 20
baseline/follow-up: baseline
disease status: Squamous Metaplasia
tissue: bronchial
gender: male
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276
Label Cy3
Label protocol DNA labeling protocol according to Enzo Life Sciences
 
Channel 2
Source name blood, pooled DNA from 19 individuals
Organism Homo sapiens
Characteristics tissue: blood
gender: female
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276
Label Cy3
Label protocol DNA labeling protocol according to Enzo Life Sciences
 
 
Hybridization protocol Hybridization protocol available via www.agilent.com
Scan protocol Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings
Description Pooled DNA from the blood of 18 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes description = Cancer 2008, 47(11): 994-1004
Data processing Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.
 
Submission date Aug 16, 2010
Last update date Aug 02, 2011
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 GPL8841
Series (1)
GSE23644 DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (test/reference)

Data table
ID_REF VALUE
A_14_P100000 -0.092085967
A_14_P100001 0.197064863
A_14_P100002 0.311492448
A_14_P100003 0.016895923
A_14_P100004 0.136987498
A_14_P100005 0.415774961
A_14_P100006 -0.474656688
A_14_P100007 -0.076635139
A_14_P100008 0.437768235
A_14_P100009 -0.151485609
A_14_P100010 -0.042862368
A_14_P100011 0.444930627
A_14_P100012 -0.108627145
A_14_P100013 0.274474635
A_14_P100014 0.657573045
A_14_P100015 0.00119781
A_14_P100016 -1.308768826
A_14_P100017 -0.099769883
A_14_P100018 0.207321427
A_14_P100019 0.364966575

Total number of rows: 43307

Table truncated, full table size 1061 Kbytes.




Supplementary file Size Download File type/resource
GSM580073_13277_S01_CGH-v4_95_Feb07_1_2_Cy3.txt.gz 14.6 Mb (ftp)(http) TXT
GSM580073_13277_S01_CGH-v4_95_Feb07_1_4_Cy3_2.txt.gz 14.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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