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Sample GSM312345 Query DataSets for GSM312345
Status Public on Apr 01, 2009
Title Chondrosarcoma_case_5
Sample type genomic
 
Channel 1
Source name Case 5
Organism Homo sapiens
Characteristics Genomic DNA from fresh frozen chondrosarcoma biopsy
Biomaterial provider Dept of Clinical Genetics, Lund University Hospital, Sweden
Extracted molecule genomic DNA
Extraction protocol DNeasy Tissue Kit (Qiagen, Valencia, CA, USA)
Label Cy3
Label protocol BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)
 
Channel 2
Source name Promega reference male DNA (Promega, Madison, WI, USA)
Organism Homo sapiens
Characteristics Pooled lymphoblastoid genomic DNA from ten male individuals
Biomaterial provider Promega, Madison, WI, USA
Extracted molecule genomic DNA
Extraction protocol none
Label Cy5
Label protocol BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)
 
 
Hybridization protocol Arrays were hybridized and washed as described in Heidenblad et al. (Oncogene 2006;25:7106-16)
Scan protocol Arrays were scanned in Agilent Microarray scanner
Description 32k BAC array CGH data on chondrosarcoma
Data processing Primary data were collected using the GenePix Pro 4.0 software, and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and lowess normalization were performed.
 
Submission date Aug 13, 2008
Last update date Feb 25, 2009
Contact name Karolin H Nord
Organization name Lund University
Department Dept of Clinical Genetics
Street address BMC C13
City Lund
ZIP/Postal code SE-22184
Country Sweden
 
Platform ID GPL4723
Series (2)
GSE12439 Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (BAC/CGH)
GSE12532 Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors

Data table header descriptions
ID_REF
VALUE log(2) ratio Cy3/Cy5

Data table
ID_REF VALUE
16114 0.463152259
21614 -0.058734344
25469 0.51595609
28383 0.509944908
8727 0.303185442
6520 -0.1245652
14569 0.442735097
10890 0.463938518
27130 0.050936085
11653 0.33770046
1416 -0.625028111
19111 -0.135212431
19756 -0.207667177
33609 -0.039720498
25591
32861
24132
32882
28512 -0.877071078
22670

Total number of rows: 31498

Table truncated, full table size 520 Kbytes.




Supplementary file Size Download File type/resource
GSM312345.gpr.gz 2.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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