NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM580072 Query DataSets for GSM580072
Status Public on Aug 02, 2011
Title Control 19 baseline Squamous Metaplasia
Sample type genomic
 
Channel 1
Source name Bronchial tissue, AFB-visualized
Organism Homo sapiens
Characteristics case number: Control 19
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 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: 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
 
 
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 -0.023964734
A_14_P100001 -0.0570294
A_14_P100002 0.304857472
A_14_P100003 0.225794236
A_14_P100004 0.306407609
A_14_P100005 0.222158123
A_14_P100006 -0.087493997
A_14_P100007 0.242004163
A_14_P100008 0.051281289
A_14_P100009 0.127843044
A_14_P100010 -0.089771561
A_14_P100011 -0.053656088
A_14_P100012 -0.250004045
A_14_P100013 0.080145063
A_14_P100014 -0.236182916
A_14_P100015 -0.02930693
A_14_P100016 -0.551853038
A_14_P100017 -0.241568841
A_14_P100018 0.09221431
A_14_P100019 0.106090935

Total number of rows: 43307

Table truncated, full table size 1059 Kbytes.




Supplementary file Size Download File type/resource
GSM580072_11618_S01_CGH-v4_95_Feb07_1_2_Cy3.txt.gz 14.5 Mb (ftp)(http) TXT
GSM580072_11618_S01_CGH-v4_95_Feb07_1_4_Cy3_2.txt.gz 14.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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