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Sample GSM1019673 Query DataSets for GSM1019673
Status Public on Jun 30, 2013
Title MDACC 10057
Sample type genomic
Source name STAG2-mutant urothelial carcinoma
Organism Homo sapiens
Characteristics patient gender: male
patient age at specimen collection: 56
procedure at collection: transurethral resection
pathologic stage at collection: pTa
stag2 mutation present in tumor: 1156C>T; 216R>Stop (nonsense)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared directly from snap-frozen urothelial carcinoma primary tumor samples using Qiagen QIAamp DNA Extraction Kits.
Label biotin
Label protocol As per manufacturer (Affymetrix).
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Urothelial carcinoma with STAG2 mutation
Data processing .CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.2 Software. Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference
The copy number data files (.CYCHP files) contain the whole genome copy number data for the 12 STAG2-mutant urothelial carcinomas of the bladder accessible using Affymetrix Chromosome Analysis Suite v1.2.2 Software.
Submission date Oct 15, 2012
Last update date Jun 30, 2013
Contact name David A. Solomon
Organization name University of California, San Francisco
Department Pathology
Street address 513 Parnassus Ave, HSW 450
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platform ID GPL16131
Series (1)
GSE41581 Frequent truncating mutations of STAG2 in bladder cancer

Data table header descriptions
VALUE genome copy number (weighted Log2 Ratio)

Data table
C-3AAAA 0.058181737
C-3AAAB -0.42870212
C-3AAAC 0.28078064
C-3AAAD -0.04722057
C-3AAAG 0.19278327
C-3AAAH 0.14194234
C-3AAAI -0.14630264
C-3AAAJ -0.40192696
C-3AAAK -0.1003041
C-3AAAL 0.12510015
C-3AAAM 0.3223348
C-3AAAN -0.24206938
C-3AAAP -0.38345346
C-3AAAQ -0.09734892
C-3AAAR 0.08955285
C-3AAAS 0.29542878
C-3AAAT -0.315172
C-3AAAU 0.13099432
C-3AAAV 0.08477525
C-3AAAW -0.103755854

Total number of rows: 2696550

Table truncated, full table size 51772 Kbytes.

Supplementary file Size Download File type/resource
GSM1019673_TW01_CytoScanHD_Array_2.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM1019673_TW01_CytoScanHD_Array_2.ChAS.cyhd.cychp.gz 80.2 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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