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Sample GSM322225 Query DataSets for GSM322225
Status Public on Dec 10, 2008
Title 3_Illumina
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics Gender: Male, Tumor content: 97%
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions. An additional purification step was performed using Phase Lock Gel Heavy (Eppendorf).
Label C-Bio and A-DNP
Label protocol Genotyping was performed using Illumina Infinium HumanHap300 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 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 rack system (Tecan, Maennedorf, Switzerland).
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 extracted from CLL patients was genotyped using Infinium HumanHap300 Duo-v2 Genotyping BeadChips (Illumina).
Data processing Image data was analyzed using Beadstudio 3.1 with GT module 3.1.12 (Illumina).
 
Submission date Sep 18, 2008
Last update date Dec 10, 2008
Contact name Richard Rosenquist Brandell
E-mail(s) richard.rosenquist@genpat.uu.se
Organization name Uppsala University
Department Genetics and Pathology
Street address Rudbeck Laboratory
City Uppsala
ZIP/Postal code SE-751 85
Country Sweden
 
Platform ID GPL6980
Series (1)
GSE13557 Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE Beadstudio confidence score
Theta Beadstudio genotype metric
R Beadstudio intensity metric
B_Allele_Freq Beadstudio estimate of B allele frequency
Log_R_Ratio Beadstudio metric for signal intensity

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
rs10000010-126_B_F_IFB1153208421:0 BB 0.9368909 0.9708627 0.9708471 0.9757907 0.005245559
rs10000023-126_B_F_IFB1153358872:0 AB 0.8234195 0.4163414 2.368272 0.4136263 -0.06206864
rs10000030-120_B_R_IFB1137703207:0 AB 0.6412052 0.7167268 0.7819412 0.4582865 0.3518421
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.02574606 0.8714929 0.01415992 -0.009322552
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.01253468 0.7909734 0.005220745 0.06877578
rs10000121-126_B_R_IFB1136471760:0 AB 0.891854 0.6548409 0.6752898 0.5076553 0.2619452
rs1000014-126_B_R_IFB1136184019:0 AA 0.7254323 0.06210243 2.267535 0.02126929 0.150559
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9613745 1.067631 0.962267 0.2230504
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.01320667 1.657073 0.0119102 -0.1014589
rs10000169-119_T_R_IFB1135612081:0 BB 0.8703538 0.990303 1.197648 0.994975 0.09135555
rs1000022-126_B_F_IFB1135126284:0 AB 0.8797732 0.634555 0.9414907 0.500543 0.1055671
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.01591703 1.375555 0.01518608 -0.4583105
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.9631054 1.092193 0.9723448 -0.1495675
rs10000300-126_T_R_IFB1152704058:0 AB 0.8601294 0.6168025 0.5932428 0.5282937 -0.2300561
rs1000031-123_B_F_IFB1135583872:0 BB 0.8717313 0.969954 1.40032 0.9827881 -0.1430722
rs1000032-126_B_R_IFB1136145093:0 BB 0.384529 0.9946992 1.063798 1 -0.09260705
rs10000388-126_B_F_IFB1135932472:0 AA 0.9530174 0.005727016 1.645342 0 0.2780529
rs1000040-126_T_F_IFB1152704061:0 AB 0.8484263 0.5905656 1.121043 0.4832803 0.1672314
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9889884 1.15504 1 -0.2711379
rs10000432-126_T_R_IFB1135756304:0 AB 0.8544981 0.7199181 0.9532177 0.5280061 0.4242063

Total number of rows: 318237

Table truncated, full table size 26910 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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