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Sample GSM471238

Query DataSets for GSM471238

Status

Public on Nov 24, 2010

Title

Normal blood DNA case 4

Sample type

genomic

Source name

Blood

Organism

Characteristics

gender: Male
tissue: Blood
disease state: normal

Extracted molecule

genomic DNA

Extraction protocol

DNA was extracted from blood sample using the DNeasy Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).

Label

unlabeled

Label protocol

unlabeled

Hybridization protocol

Hybridization was done according to the Infinium HD Super Assay Manual EUC EUC 11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

Scan protocol

Scanning was done according to the Infinium HD Super Assay Manual EUC EUC 11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

Description

Genomic DNA extracted from normal blood were analyzed for DNA copy number aberrations using Illumina Human CNV370-Quad v3.0 BeadChips (Illumina). The results were compared to the DNA copy number aberrations found in the corresponding tumour samples, analyzed using the same platform.

Data processing

Genomic DNA extracted from hibernoma biopsies was analyzed for DNA copy number aberrations using Illumina Human1M-Duo v3.0 BeadChips (Illumina).

Submission date

Nov 16, 2009

Last update date

Nov 24, 2010

Contact name

Karolin H Nord

Organization name

Lund University

Department

Dept of Clinical Genetics

Street address

BMC C13

City

Lund

ZIP/Postal code

SE-22184

Country

Sweden

Platform ID

Series (1)

Concomitant deletions of tumor suppressor genes MEN1 and AIP are essential for the pathogenesis of the brown fat tumor hibernoma

Data table header descriptions
ID_REF
X Raw
Y Raw
X
Y
VALUE	B allele frequency
Log R Ratio

Data table
ID_REF	X Raw	Y Raw	X	Y	VALUE	Log R Ratio
rs12354060-128_T_F_1514243431	1103	12370	0.1024585	1.538681	1	-0.04998357
rs2691310-128_B_R_1514251078	408	9536	0.0271888	1.18637	1	-0.4266413
rs2531266-128_T_R_1514250574	5097	9360	0.6281886	1.16656	0.5433167	-0.06273368
rs4124251-128_B_F_1514285504	11168	1490	1.291655	0.1804883	0.008076465	0.06707931
rs8179466-128_B_F_1514290736	1357	10772	0.134996	1.339738	1	0.006227104
rs6603779-128_B_F_1514258763	15279	9032	1.75449	1.117077	0.5985663	-0.05260767
cnvi0007379-126_B_F_1514269226	2452	13778	0.2563723	1.713273	1	-0.1464022
cnvi0019140-126_B_R_1525540355	8146	932	0.9419032	0.1123973	0	-0.1118854
cnvi0007389-126_T_R_1514269233	9360	503	1.083653	0.05848188	0.002021055	-0.19326
cnvi0021559-126_T_F_1525544132	25783	3903	2.983668	0.4742545	0	-0.1441089
cnvi0007392-126_B_F_1514269234	16489	1392	1.909544	0.1659393	0.005087344	0.120979
cnvi0007380-126_B_F_1514269227	12972	118	1.503696	0.00897957	0	-0.04548328
cnvi0021553-126_T_R_1525544974	13688	339	1.586393	0.03616039	0	0.06851114
cnvi0007381-126_B_R_1514269228	14413	1044	1.669211	0.1235586	0.007150541	-0.004215083
cnvi0019138-126_B_R_1525543195	454	12475	0.02533241	1.514426	1	0.07065311
cnvi0021554-126_T_F_1525544906	12236	859	1.416841	0.1015038	0.007249685	-0.02887784
cnvi0019139-126_B_R_1525539977	404	8297	0.02909017	1.03221	0.9956496	0.05668385
cnvi0023337-126_B_F_1525548141	590	9814	0.04778594	1.220879	1	-0.05147458
cnvi0007382-126_T_R_1514269229	2696	11636	0.2887876	1.446648	0.9709425	0.007605285
cnvi0007383-126_B_F_1514233811	12033	978	1.393048	0.1164002	0.01419045	-0.2221938

Total number of rows: 373397

Table truncated, full table size 27997 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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