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Sample GSM400864 Query DataSets for GSM400864
Status Public on May 09, 2009
Title ccRCC tumor and normal blood DNA pair 32
Sample type genomic
 
Source name ccRCC tumor and blood
Organism Homo sapiens
Characteristics gender: male
tissue: ccRCC tumor and blood
disease state: carcinoma
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA from fresh frozen tissue was performed using QIAamp DNeasy Blood and Tissue kit (QIAGEN, Valencia, CA).
Label C-Bio and A-DNP
Label protocol 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber.
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description Genomic DNA from ccRCC tumor and reference DNA from blood sample of the corresponding ccRCC patient were genotyped using Infinium HumanHap300 Genotyping BeadChips (Illumina).
Data processing Genomic DNA extracted from ccRCC tumor and normal blood DNA pairs was genotyped using Infinium HumanHap300 Genotyping BeadChips (Illumina).
 
Submission date May 07, 2009
Last update date May 08, 2009
Contact name Xifeng Wu
E-mail(s) xwu@mdanderson.org
Phone 7137452485
Fax 7137924657
Organization name UT M.D Anderson Cancer Center
Department Epidemiology
Street address 1155 pressler blvd.
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6979
Series (1)
GSE16019 Profiling of chromosomal alterations in renal cell carcinoma using high-density single nucleotide polymorphism arrays

Data table header descriptions
ID_REF
VALUE Log_R_Ratio
AlleleFreq Ref.
AlleleFreq Sub.
|dAlleleFreq sub-ref|

Data table
ID_REF VALUE AlleleFreq Ref. AlleleFreq Sub. |dAlleleFreq sub-ref|
rs3934834-124_T_R_1135975865 -0.000254869 0.485538 0.5430231 0.05748513
rs3737728-124_T_R_1135790679 -0.3716319 1 1
rs6687776-124_T_R_1135347468 -0.252096 0.5336909 0.5721039 0.03841299
rs9651273-124_T_F_1136827223 -0.3669004 1 1
rs4970405-124_T_F_1136522326 -0.03740425 0 8.63E-05
rs12726255-124_B_R_1135572792 0.2010775 0.6070161 0.5659451 0.04107094
rs2298217-124_T_R_1135807872 0.05493586 1 1
rs4970357-124_T_F_1135327694 0.2901763 0.07685652 0.04531674
rs4970362-124_T_F_1135713090 0.1404523 0.9932694 1
rs9660710-124_B_R_1135732876 0.3091374 0.9992528 1
rs4970420-124_B_R_1136441302 -0.1539143 1 1
rs1320565-124_B_F_1137428853 0.2555923 0 0
rs11260549-124_B_R_1135739417 -0.0767766 1 1
rs9729550-124_B_R_1135710069 0.08475299 0.6944818 0.6761706 0.01831114
rs11721-124_T_R_1136433517 -0.01553329 1 1
rs2887286-124_B_R_1135111632 0.2606548 0.5384167 0.5075877 0.03082901
rs3813199-124_T_R_1136807858 0.04075658 1 0.9988415
rs3766186-124_T_R_1136764966 0.2866704 1 1
rs7515488-124_B_F_1136819717 -0.3446363 0.7832823 0.5744688 0.2088135
rs715643-124_T_R_1137448467 -0.03748384 1 1

Total number of rows: 317497

Table truncated, full table size 17912 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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