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Sample GSM580109 Query DataSets for GSM580109
Status Public on Aug 02, 2011
Title Case 01 distinct site Right Bronchus 6
Sample type genomic
 
Channel 1
Source name Bronchial tissue, AFB-visualized
Organism Homo sapiens
Characteristics case number: Case 01
tissue type: distinct site Right Bronchus 6
tissue: bronchial
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 Cy5
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 -0.085003613
A_14_P100001 0.330447918
A_14_P100002 0.263177451
A_14_P100003 0.05336795
A_14_P100004 -0.121433024
A_14_P100005 0.486833693
A_14_P100006 -0.833913957
A_14_P100007 0.337693133
A_14_P100008 0.227172309
A_14_P100009 -0.370392852
A_14_P100010 0.367987527
A_14_P100011 0.128979714
A_14_P100012 0.098604287
A_14_P100013 0.127894703
A_14_P100014 0.173853031
A_14_P100015 -0.464005895
A_14_P100016 -0.505745459
A_14_P100017 -0.131875583
A_14_P100018 0.419843689
A_14_P100019 0.104046548

Total number of rows: 43307

Table truncated, full table size 1060 Kbytes.




Supplementary file Size Download File type/resource
GSM580109_251495023534_251495023534_S01_CGH-v4_95_Feb07_1_1_Cy5.txt.gz 14.6 Mb (ftp)(http) TXT
GSM580109_251495023534_251495023534_S01_CGH-v4_95_Feb07_1_4_Cy3_3.txt.gz 14.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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