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Sample GSM580085 Query DataSets for GSM580085
Status Public on Aug 02, 2011
Title Control 03 follow up Normal
Sample type genomic
 
Channel 1
Source name Bronchial tissue, AFB-visualized
Organism Homo sapiens
Characteristics case number: Control 03
baseline/follow-up: follow up
disease status: Normal
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 -0.144833934
A_14_P100001 0.179678089
A_14_P100002 0.379493271
A_14_P100003 0.011235426
A_14_P100004 -0.554228907
A_14_P100005 -0.121338994
A_14_P100006 -0.216936575
A_14_P100007 -0.232987616
A_14_P100008 0.469321922
A_14_P100009 0.027292404
A_14_P100010 0.213329354
A_14_P100011 0.616962741
A_14_P100012 0.067282582
A_14_P100013 0.291097279
A_14_P100014 0.47641328
A_14_P100015 0.179154277
A_14_P100016 -0.911408709
A_14_P100017 -0.230842784
A_14_P100018 0.097451685
A_14_P100019 0.162571395

Total number of rows: 43307

Table truncated, full table size 1061 Kbytes.




Supplementary file Size Download File type/resource
GSM580085_13277_S01_CGH-v4_95_Feb07_1_1_Cy3.txt.gz 14.6 Mb (ftp)(http) TXT
GSM580085_13277_S01_CGH-v4_95_Feb07_1_4_Cy3_1.txt.gz 14.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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