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Sample GSM869190 Query DataSets for GSM869190
Status Public on Aug 31, 2012
Title Human Colon Tumor Tissue 72
Sample type genomic
 
Channel 1
Source name Human Colon Tumor Tissue 72
Organism Homo sapiens
Characteristics gender: M
age (y): 65
braf/kras mutation: Wild type
tumor location: rectum
tissue: colon tumor
pathology: T-ad potion
cimp: CIMP-L
Growth protocol A total of 84 colorectal tumor specimens were obtained from endoscopic biopsy.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.
Label Cy5
Label protocol Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.
 
Channel 2
Source name Human Genomic DNA (Promega)
Organism Homo sapiens
Characteristics sample type: Human Genomic DNA (Promega)
Growth protocol A total of 84 colorectal tumor specimens were obtained from endoscopic biopsy.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.
Label Cy3
Label protocol Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.
 
 
Hybridization protocol Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.
Scan protocol Array was scanned with an Agilent G2565BA Microarray Scanner.
Data processing Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.
 
Submission date Feb 01, 2012
Last update date Aug 31, 2012
Contact name Eiichiro Yamamoto
E-mail(s) eiichiro@xa3.so-net.ne.jp
Phone +81-11-611-2111
Organization name Sapporo medical university
Street address South-1, West-16, Chuo-ku
City Sapporo
ZIP/Postal code 060-8543
Country Japan
 
Platform ID GPL10123
Series (2)
GSE35476 Array CGH analysis of human colorectal tumors
GSE35534 Genome-wide copy number aberrations and methylation profiles in human colorectal lesions

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.275136874e-002
2 1.728413565e-001
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 2.119285373e-001
12 0.000000000e+000
13 8.034859830e-002
14 0.000000000e+000
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4226 Kbytes.




Supplementary file Size Download File type/resource
GSM869190_sample_44-2.txt.gz 50.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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