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Sample GSM412120

Query DataSets for GSM412120

Status

Public on Dec 03, 2009

Title

NA15510_3 (Illumina)

Sample type

genomic

Source name

Hapmap

Organism

Characteristics

sample: NA15510

Biomaterial provider

Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA15510

Extracted molecule

genomic DNA

Extraction protocol

Genomic DNA from breast tumors and matched normals was extracted with Qiagen's Dneasy kit. The extractions were not done manually but using Qiagen's Quiacube. Input = 20x10um sections per sample.

Label

Biotin

Label protocol

post-hybridization labelling: single base extension using labled dNTPs

Hybridization protocol

Manufacturers instructions: 1. denature 750ng DNA, 2. whole genome ampliofication, 3. frangemtation of the DNA, 4. hybridization to 50mers on array

Scan protocol

Manufacturers default

Description

Genomic DNA extracted from a hapmap sample was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).

Data processing

Data were processed using BeadStudio Genotyping Module 3.2.32

Submission date

Jun 03, 2009

Last update date

Dec 09, 2009

Contact name

Christina Curtis

E-mail(s)

christina.curtis@cancer.org.uk

Phone

01223404231

Fax

1223 404208

Organization name

University of Cambridge

Department

Computational Biology/Oncology

Lab

Tavaré

Street address

Robinson Way

City

Cambridge

ZIP/Postal code

CB20RE

Country

United Kingdom

Platform ID

Series (1)

The pitfalls of platform comparison: DNA copy number array technologies assessed

Data table header descriptions
ID_REF
GTYpe	GTYpe: The genotype of this SNP for the sample.
Score
Theta	The normalized Theta-value of this SNP for the sample.
R	The normalized R-value of this SNP for the sample
B Allele Freq	The normalized intensity of the B allele.
VALUE	Log R Ratio: The base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the clusters).

Data table
ID_REF	GTYpe	Score	Theta	R	B Allele Freq	VALUE
rs10000010-126_B_F_IFB1153208421:0	AB	0.9368909	0.5360937	0.9430267	0.4634165	-0.1306202
rs10000023-126_B_F_IFB1153358872:0	AB	0.8234195	0.5130802	2.387082	0.5168719	-0.04064669
rs10000030-120_B_R_IFB1137703207:0	AB	0.8158658	0.7635026	0.695285	0.4908531	0.1467358
rs1000007-123_T_F_IFB1152225452:0	AB	0.8747823	0.6356922	1.230376	0.4836698	0.2414829
rs10000092-123_T_R_IFB1153358875:0	AA	0.9264655	0.005717642	0.903998	0	0.2610938
rs10000121-126_B_R_IFB1136471760:0	AA	0.891854	0.01601069	0.4289502	0.005905971	-0.137678
rs1000014-126_B_R_IFB1136184019:0	BB	0.7254323	0.9634347	1.5054	0.99743	0.09278569
rs10000141-126_T_F_IFB1137734411:0	BB	0.8891098	0.9887241	1.052955	1	0.1950605
rs1000016-126_B_R_IFB1156563530:0	AA	0.875866	0.006963545	1.613583	0.005332851	-0.1398177
rs10000169-119_T_R_IFB1135612081:0	AA	0.8703538	0.01234673	1.012846	0.004333222	0.01333102
rs1000022-126_B_F_IFB1135126284:0	AB	0.8797732	0.6381557	1.03239	0.5057306	0.2386354
rs10000272-126_T_R_IFB1136539894:0	AA	0.8434824	0.004558623	1.621306	0.003135974	-0.2204812
rs10000282-121_T_R_IFB1136743500:0	BB	0.8183947	0.9905075	1.186314	1	-0.01486042
rs10000300-126_T_R_IFB1152704058:0	BB	0.8601294	0.9935675	0.71507	1	0.01494892
rs1000031-123_B_F_IFB1135583872:0	AB	0.8717313	0.4488572	2.401193	0.4834217	0.05146553
rs1000032-126_B_R_IFB1136145093:0	AB	0.384529	0.7214813	1.05379	0.4967363	-0.08652792
rs10000388-126_B_F_IFB1135932472:0	AB	0.9530174	0.5241453	1.30628	0.5058571	-0.09918348
rs1000040-126_T_F_IFB1152704061:0	AB	0.8484263	0.6055793	1.325782	0.4958538	0.4029115
rs1000041-126_T_F_IFB1153889147:0	AB	0.8351063	0.5188631	1.904326	0.524577	0.01952167
rs10000432-126_T_R_IFB1135756304:0	AB	0.8544981	0.7423248	0.9250427	0.5696115	0.365087

Total number of rows: 370404

Table truncated, full table size 30653 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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