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Sample GSM322220 Query DataSets for GSM322220
Status Public on Dec 10, 2008
Title 4_Illumina
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics Gender: Male, Tumor Content: 93%
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 AB 0.9368909 0.5908185 1.063341 0.5150617 0.03596429
rs10000023-126_B_F_IFB1153358872:0 AA 0.8234195 0.02465049 2.508281 0 0.04323239
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9773427 0.7624532 0.9789704 -0.004901192
rs1000007-123_T_F_IFB1152225452:0 AB 0.8747823 0.6646964 1.002666 0.5115334 -0.06008751
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.02525284 0.7545648 0.01809399 0.001486459
rs10000121-126_B_R_IFB1136471760:0 AA 0.891854 0.01653459 0.443195 0.006314455 -0.09077454
rs1000014-126_B_R_IFB1136184019:0 AB 0.7254323 0.4050711 1.969754 0.4314837 -0.1156538
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9782013 0.9952147 0.9891185 0.1167768
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.01227499 1.477491 0.01092863 -0.266945
rs10000169-119_T_R_IFB1135612081:0 AB 0.8703538 0.6577364 1.377322 0.5196074 0.1604155
rs1000022-126_B_F_IFB1135126284:0 BB 0.8797732 0.9695852 0.9494262 0.9832298 0.1269556
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.01534732 1.797294 0.01458168 -0.0724638
rs10000282-121_T_R_IFB1136743500:0 AB 0.8183947 0.6472936 1.208726 0.5790755 -0.1703527
rs10000300-126_T_R_IFB1152704058:0 AB 0.8601294 0.5883337 0.624641 0.493241 -0.1530561
rs1000031-123_B_F_IFB1135583872:0 BB 0.8717313 0.9698512 1.616174 0.98269 0.06360684
rs1000032-126_B_R_IFB1136145093:0 NC 0.02768335 0.6225353 1.211299 0.4218904 0.1115917
rs10000388-126_B_F_IFB1135932472:0 AA 0.9530174 0.009024452 1.476197 0.001959338 0.1212407
rs1000040-126_T_F_IFB1152704061:0 AA 0.8484263 0.01045037 1.449868 0 0.8065506
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9744353 1.427396 0.992505 0.01885208
rs10000432-126_T_R_IFB1135756304:0 AB 0.8544981 0.7270339 0.7486138 0.5412189 0.07057499

Total number of rows: 318237

Table truncated, full table size 26858 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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