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Sample GSM756104 Query DataSets for GSM756104
Status Public on Oct 04, 2012
Title flat adenoma 120
Sample type genomic
 
Channel 1
Source name Colorectal tissue, macrodissected [test]
Organism Homo sapiens
Characteristics gender: M
paris classification: IIa
Extracted molecule genomic DNA
Extraction protocol Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).
Label Cy3
Label protocol DNA labeling protocol according to Enzo Life Sciences.
 
Channel 2
Source name FFPE colon DNA pool from healthy individuals [reference]
Organism Homo sapiens
Characteristics gender: M
reference description: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004
Extracted molecule genomic DNA
Extraction protocol Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).
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 v10.5 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings
Description raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_120
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 Jul 07, 2011
Last update date Oct 04, 2012
Contact name Daoud Sie
E-mail(s) [email protected]
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 GPL8687
Series (1)
GSE30479 DNA copy number changes in colorectal flat adenomas

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

Data table
ID_REF VALUE
81584 -0.596
115021 -0.303
59850 0.439
123164 -0.137
140376 0.363
111805 -0.040
91785 0.615
55410 0.251
49634 -0.150
61425 0.146
178535 0.359
70828 0.118
177952 0.364
122808 0.159
64151 0.170
60883 -0.220
129698 0.691
140610 -0.283
180564 0.054
37368 -0.119

Total number of rows: 173370

Table truncated, full table size 2185 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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