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Sample GSM322223 Query DataSets for GSM322223
Status Public on Dec 10, 2008
Title 7_Illumina
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics Gender: Female, Tumor content: 92%
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 0.9981979 0.8733732 1 -0.1398892
rs10000023-126_B_F_IFB1153358872:0 BB 0.8234195 0.9781999 1.582601 0.9972878 -0.1414022
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9813017 0.8016609 0.9884185 0.06251449
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.02522105 0.8525687 0.01375579 -0.04076369
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.006923629 0.6624427 0 -0.1873642
rs10000121-126_B_R_IFB1136471760:0 AA 0.891854 0.02668053 0.5029967 0.01422527 0.08742151
rs1000014-126_B_R_IFB1136184019:0 BB 0.7254323 0.9362235 1.186757 0.970417 -0.2907136
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9895278 0.9754094 1 0.08446117
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.007920782 1.713129 0.006341333 -0.05345346
rs10000169-119_T_R_IFB1135612081:0 AA 0.8703538 0.009103909 1.189455 0.001788616 0.2469402
rs1000022-126_B_F_IFB1135126284:0 BB 0.8797732 0.9682712 0.8967712 0.9813367 0.04460306
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.0130239 1.591581 0.01211677 -0.2476895
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.9812686 1.115078 0.9949628 -0.1094291
rs10000300-126_T_R_IFB1152704058:0 AB 0.8601294 0.6038058 0.6965109 0.5104389 0.002318205
rs1000031-123_B_F_IFB1135583872:0 BB 0.8717313 0.9702587 1.50344 0.983079 -0.04012649
rs1000032-126_B_R_IFB1136145093:0 NC 0.01019927 0.6106683 1.131168 0.4129139 0.01250888
rs10000388-126_B_F_IFB1135932472:0 AB 0.9530174 0.5114426 1.256131 0.4929713 -0.1582284
rs1000040-126_T_F_IFB1152704061:0 AB 0.823985 0.5023792 1.048927 0.4094268 0.1090021
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9888678 1.259903 1 -0.1458969
rs10000432-126_T_R_IFB1135756304:0 BB 0.8544981 1 0.7748798 1 -0.06105419

Total number of rows: 318237

Table truncated, full table size 26824 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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