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Sample GSM400892 Query DataSets for GSM400892
Status Public on May 09, 2009
Title ccRCC tumor and normal blood DNA pair 60
Sample type genomic
 
Source name ccRCC tumor and blood
Organism Homo sapiens
Characteristics gender: female
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 -0.2192296 1 1
rs3737728-124_T_R_1135790679 -0.05901373 0.5623795 0.5059711 0.05640841
rs6687776-124_T_R_1135347468 0.1372942 1 0.9968503
rs9651273-124_T_F_1136827223 -0.000985498 0.5289003 0.4937477 0.03515258
rs4970405-124_T_F_1136522326 -0.4284942 0.01135408 0.02571547
rs12726255-124_B_R_1135572792 -0.1558363 0.005574604 0
rs2298217-124_T_R_1135807872 0.2974674 1 0.9956741
rs4970357-124_T_F_1135327694 -1.304275 0.01330571 0.06482393
rs4970362-124_T_F_1135713090 -0.1139026 0.4701424 0.4805242 0.01038185
rs9660710-124_B_R_1135732876 -0.13632 0.998933 1
rs4970420-124_B_R_1136441302 0.00226019 1 0.9855053
rs1320565-124_B_F_1137428853 -0.0894559 1 0.9961677
rs11260549-124_B_R_1135739417 0.08557761 0.9724215 0.991247
rs9729550-124_B_R_1135710069 -0.1569509 0 0
rs11721-124_T_R_1136433517 0.009731861 0.5182182 0.5139264 0.004291773
rs2887286-124_B_R_1135111632 -0.09829986 0 0.002294907
rs3813199-124_T_R_1136807858 -0.245946 0.4778258 0.5060731 0.02824733
rs3766186-124_T_R_1136764966 -0.187929 0.4555859 0.4703096 0.01472375
rs7515488-124_B_F_1136819717 -0.365052 0.4217188 0.5641999 0.142481
rs715643-124_T_R_1137448467 -0.09449782 1 1

Total number of rows: 317497

Table truncated, full table size 19069 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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