NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM580052 Query DataSets for GSM580052
Status Public on Aug 02, 2011
Title Case 01 baseline Squamous Metaplasia
Sample type genomic
 
Channel 1
Source name Bronchial tissue, AFB-visualized
Organism Homo sapiens
Characteristics case number: Case 01
baseline/follow-up: baseline
disease status: Squamous Metaplasia
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 Cy5
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 -0.117694619
A_14_P100001 -0.207803339
A_14_P100002 0.033016333
A_14_P100003 0.22628851
A_14_P100004 0.007873932
A_14_P100005 0.361720777
A_14_P100006 -0.351688071
A_14_P100007 -0.001054775
A_14_P100008 0.480889625
A_14_P100009 -0.755099068
A_14_P100010 0.974645861
A_14_P100011 0.576539782
A_14_P100012 0.36820095
A_14_P100013 -0.335120665
A_14_P100014 0.474638417
A_14_P100015 -0.539795621
A_14_P100016 -0.61628322
A_14_P100017 -0.536900329
A_14_P100018 0.494615272
A_14_P100019 0.204552477

Total number of rows: 43307

Table truncated, full table size 1060 Kbytes.




Supplementary file Size Download File type/resource
GSM580052_251495017098_251495017098_S01_CGH-v4_95_Feb07_1_1_Cy5.txt.gz 14.6 Mb (ftp)(http) TXT
GSM580052_251495017098_251495017098_S01_CGH-v4_95_Feb07_1_4_Cy5.txt.gz 14.6 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap