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Sample GSM471232

Query DataSets for GSM471232

Status

Public on Nov 24, 2010

Title

Hibernoma case 1 (CNV370-Quad)

Sample type

genomic

Source name

Hibernoma

Organism

Characteristics

gender: Female
tissue: Hibernoma
disease state: soft tissue tumour

Extracted molecule

genomic DNA

Extraction protocol

DNA was extracted from fresh frozen tumour biopsies using the DNeasy Tissue 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 hibernoma biopsies were analyzed for DNA copy number aberrations using Illumina Human CNV370-Quad v3.0 BeadChips (Illumina).

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	1169	16802	0.09201245	1.558698	1	-0.04159429
rs2691310-128_B_R_1514251078	421	11905	0.02272649	1.104167	1	-0.5335343
rs2531266-128_T_R_1514250574	7380	12769	0.6657912	1.163738	0.5161934	-0.03504305
rs4124251-128_B_F_1514285504	14494	3521	1.466034	0.3234044	0.06815259	0.3486686
rs8179466-128_B_F_1514290736	3879	14660	0.3706798	1.359372	0.9468563	0.2365872
rs6603779-128_B_F_1514258763	19045	7424	1.923583	0.6850111	0.3415736	-0.1911736
cnvi0007379-126_B_F_1514269226	2682	19127	0.242698	1.774306	1	-0.112124
cnvi0019140-126_B_R_1525540355	11067	1533	1.120168	0.1394052	0	0.1447636
cnvi0007389-126_T_R_1514269233	10876	767	1.101803	0.06831881	0.007885243	-0.1583344
cnvi0021559-126_T_F_1525544132	28555	5409	2.89384	0.4963365	0.003784556	-0.1726541
cnvi0007392-126_B_F_1514269234	18998	1645	1.926836	0.1484742	0	0.1208586
cnvi0007380-126_B_F_1514269227	14109	285	1.431367	0.02302611	0	-0.1021689
cnvi0021553-126_T_R_1525544974	13223	549	1.340867	0.04768541	0.007432336	-0.1561734
cnvi0007381-126_B_R_1514269228	16519	1015	1.675522	0.09039815	0	-0.02598443
cnvi0019138-126_B_R_1525543195	383	16331	0.0001700867	1.486651	1	0.02018036
cnvi0021554-126_T_F_1525544906	13034	829	1.321251	0.07371338	0	-0.1511494
cnvi0019139-126_B_R_1525539977	277	7960	0.01356209	0.7379215	1	-0.4413348
cnvi0023337-126_B_F_1525548141	729	12479	0.0532614	1.157407	0.9952664	-0.1189818
cnvi0007382-126_T_R_1514269229	2926	16289	0.2714659	1.510774	0.9876065	0.04599923
cnvi0007383-126_B_F_1514233811	14412	1266	1.460827	0.1140552	0.01015249	-0.1609705

Total number of rows: 373397

Table truncated, full table size 27973 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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