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Sample GSM735771 Query DataSets for GSM735771
Status Public on Oct 26, 2012
Title HCC tissue27643
Sample type genomic
 
Source name HCC patients
Organism Homo sapiens
Characteristics tissue: Hepatocellular carcinoma
Extracted molecule genomic DNA
Extraction protocol HCC Tumor cells were manually microdissected from three consecutive 10-μm sections for each sample under a dissecting microscope to obtain high-purity (>80%) tumor DNA. Fixative removal was performed twice in xylene and absolute ethanol washes. The pellets were digested with proteinase K and then processed according to the QIAamp DNA FFPE Tissue protocol (Qiagen Inc. GmbH, Germany). The concentration was determined by Nanodrop (Thermo Scientific Inc., Wilmington, DE, USA)
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol Formalin-fixed paraffin-embedded tumor DNA was hybridized on Affymetrix GeneChip Human Mapping SNP6.0 using the Human mapping SNP6.0 assay kit (Affymetrix Inc., Santa Clara, USA) and following the manufacturer’s protocol. The only modification to the manufacturer’s protocol occurred after digestion and adaptor ligation, when the DNA was split into nine plates instead of three. Independent PCR reactions were set up using TITANIUM Taq DNA polymerase (Clontech Laboratories, Inc. Mountain View, USA), for the recommended 35 cycles. The nine PCR products were then pooled.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to SNP 6.0
Data processing CEL files (generated by Affymetrix GTYPE using the DM algorithm) were processed by Genotyping Console 3.0.1. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758.
 
Submission date Jun 01, 2011
Last update date Oct 26, 2012
Contact name jie hu
Organization name Zhongshan hospital, Fudan University
Street address 180 Fenglin Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL6801
Series (1)
GSE29667 Affymetrix SNP array data for hepatocellular carcinoma tissue

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.031219 AA 3938.301270 1467.967529
SNP_A-1967418 BB 0.089614 BB 640.416199 1378.340942
SNP_A-1969580 BB 0.002507 BB 1185.260132 4581.477051
SNP_A-4263484 BB 0.010717 BB 1056.993774 3488.060547
SNP_A-1978185 AB 0.007496 AB 738.686584 653.077454
SNP_A-4264431 AA 0.001343 AA 3074.788086 828.489319
SNP_A-1980898 BB 0.014578 BB 441.120453 808.080994
SNP_A-1983139 AB 0.004124 AB 3106.274902 2916.825439
SNP_A-4265735 NC 0.261393 AA 3725.453857 1316.443726
SNP_A-1995832 AB 0.021614 AB 1448.853271 1745.127441
SNP_A-1995893 BB 0.001487 BB 932.501465 1999.136719
SNP_A-1997689 AB 0.006119 AB 1194.255737 1595.089233
SNP_A-1997709 AB 0.026807 AB 1246.710693 600.642456
SNP_A-1997896 NC 0.183707 AB 1279.402954 988.695129
SNP_A-1997922 BB 0.087785 BB 701.919556 1111.141479
SNP_A-2000230 NC 0.469149 AB 2632.722412 1513.449463
SNP_A-2000332 AB 0.007834 AB 1229.809570 1168.499634
SNP_A-2000337 AB 0.023280 AB 329.060486 723.923462
SNP_A-2000342 AA 0.053877 AA 1091.718872 1031.280884
SNP_A-4268173 NC 0.144345 AA 391.524139 449.072113

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM735771.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM735771.chp.gz 12.5 Mb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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