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Sample GSM937065 Query DataSets for GSM937065
Status Public on Jan 16, 2013
Title SCC of the vulva 09-818 aCGH
Sample type genomic
 
Channel 1
Source name tumor tissue
Organism Homo sapiens
Characteristics differentiation: moderately differentiated
tissue: squamous cell carcinoma tumor
individual: 09-818
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from fresh-frozen tissue using the MagAttract DNA Mini M48 kit (Qiagen Inc., Valencia, CA, USA).
Label Cy3
Label protocol DNA was labeled according to the manufacturer’s instructions.
 
Channel 2
Source name control DNA (supplied by Agilent)
Organism Homo sapiens
Characteristics sample type: Cat nr G1521 Human Genomic DNA Female from Promega
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from fresh-frozen tissue using the MagAttract DNA Mini M48 kit (Qiagen Inc., Valencia, CA, USA).
Label Cy5
Label protocol DNA was labeled according to the manufacturer’s instructions.
 
 
Hybridization protocol aCGH was performed using Agilent SurePrint G3 Human CGH Microarray 4 x 180K arrays (Agilent Technologies Inc., Palo Alto, CA, USA).
Scan protocol All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.
Data processing Genomic Workbench software (Agilent Technologies Inc.) was used with design file 022060.xml.
 
Submission date May 24, 2012
Last update date Jan 20, 2013
Contact name Francesca Micci
E-mail(s) francesca.micci@medisin.uio.no
Organization name Oslo Universitetssykehus
Department Institute for medical informatics
Lab cancer cytogenetics
Street address Ullernchausseen 70
City oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL10123
Series (2)
GSE38229 aCGH was used to identify the overall genomic imbalances of SCC of the vulva in 14 patients
GSE38230 SCC of the vulva

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

Data table
ID_REF VALUE
1 9.412123821e-003
2 0.000000000e+000
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 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
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 4214 Kbytes.




Supplementary file Size Download File type/resource
GSM937065_US83800213_252206011662_S01_CGH_105_Dec08_1_2_09_818.txt.gz 50.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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