GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM322222

Query DataSets for GSM322222

Status

Public on Dec 10, 2008

Title

8_Illumina

Sample type

genomic

Source name

Blood

Organism

Characteristics

Gender: Female, Tumor content: 87%

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

Series (1)

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	0.5352184	1.115317	0.4626596	0.1116672
rs10000023-126_B_F_IFB1153358872:0	AA	0.8234195	0.03442591	2.372272	0.003355507	-0.03776151
rs10000030-120_B_R_IFB1137703207:0	BB	0.8158658	0.9789866	0.8228439	0.9828935	0.1030207
rs1000007-123_T_F_IFB1152225452:0	AA	0.8747823	0.03308935	0.862623	0.01981247	-0.02731723
rs10000092-123_T_R_IFB1153358875:0	AA	0.9264655	0.01201372	0.7596215	0.004693426	0.01039883
rs10000121-126_B_R_IFB1136471760:0	BB	0.891854	0.985867	0.7171453	1	0.1937261
rs1000014-126_B_R_IFB1136184019:0	BB	0.7254323	0.9416332	1.429276	0.9757872	-0.01451651
rs10000141-126_T_F_IFB1137734411:0	BB	0.8891098	0.9835371	0.9422281	0.9976331	0.03628251
rs1000016-126_B_R_IFB1156563530:0	AA	0.875866	0.006078671	1.797018	0.004400606	0.01552057
rs10000169-119_T_R_IFB1135612081:0	AA	0.8703538	0.01400603	1.078506	0.005635263	0.1030692
rs1000022-126_B_F_IFB1135126284:0	AB	0.8797732	0.6393031	0.8304154	0.5073837	-0.0754154
rs10000272-126_T_R_IFB1136539894:0	AA	0.8434824	0.01253435	1.694334	0.01159741	-0.1574018
rs10000282-121_T_R_IFB1136743500:0	BB	0.8183947	0.978533	1.085368	0.9915562	-0.1499345
rs10000300-126_T_R_IFB1152704058:0	AB	0.8601294	0.599902	0.5946139	0.5050759	-0.2256189
rs1000031-123_B_F_IFB1135583872:0	BB	0.8717313	0.9722595	1.422274	0.9849888	-0.1173365
rs1000032-126_B_R_IFB1136145093:0	BB	0.384529	0.9892818	0.977489	1	-0.2142825
rs10000388-126_B_F_IFB1135932472:0	BB	0.9530174	0.99044	1.240358	1	0.1287876
rs1000040-126_T_F_IFB1152704061:0	AA	0.8484263	0.0275951	1.088684	0.01180926	0.384528
rs1000041-126_T_F_IFB1153889147:0	BB	0.8351063	0.968279	1.247508	0.9861817	-0.1819721
rs10000432-126_T_R_IFB1135756304:0	AA	0.8544981	0.02601414	0.6798906	0.004254551	0.4148666

Total number of rows: 318237

Table truncated, full table size 26882 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |