GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM412092

Query DataSets for GSM412092

Status

Public on Dec 03, 2009

Title

SUM159dil_1 (Illumina)

Sample type

genomic

Source name

Cell Line

Organism

Characteristics

sample: SUM159dil

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

30% cell line DNA mixed with 70% normal breast DNA

Data processing

Data were processed using BeadStudio Genotyping Module 3.2.32

Submission date

Jun 03, 2009

Last update date

Dec 02, 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	AA	0.9368909	0.001502903	0.9037312	0.001079583	-0.06176824
rs10000023-126_B_F_IFB1153358872:0	AB	0.8234195	0.4719873	2.160723	0.4734036	-0.197549
rs10000030-120_B_R_IFB1137703207:0	BB	0.8158658	0.9905565	0.7886365	1	0.02742887
rs1000007-123_T_F_IFB1152225452:0	NC	0	0.1323771	1.091857	0.09623986	0.2696088
rs10000092-123_T_R_IFB1153358875:0	AB	0.9264655	0.5777231	1.081033	0.5812041	0.5717621
rs10000121-126_B_R_IFB1136471760:0	AB	0.891854	0.6199913	0.613711	0.476831	0.1374421
rs1000014-126_B_R_IFB1136184019:0	AB	0.7254323	0.5159585	1.895114	0.5532125	-0.1276884
rs10000141-126_T_F_IFB1137734411:0	BB	0.8891098	0.9949718	0.9710106	1	0.07634948
rs1000016-126_B_R_IFB1156563530:0	AA	0.875866	0.001935643	1.406407	3.578742E-05	-0.3380635
rs10000169-119_T_R_IFB1135612081:0	AA	0.8703538	0.01179552	1.06439	0.003900697	0.08523677
rs1000022-126_B_F_IFB1135126284:0	NC	0.00738825	0.1281671	0.8473794	0.09420884	0.06544194
rs10000272-126_T_R_IFB1136539894:0	AA	0.8434824	0.004800711	1.758453	0.003392803	-0.103346
rs10000282-121_T_R_IFB1136743500:0	AB	0.6831599	0.677559	1.307045	0.6167639	-0.04233492
rs10000300-126_T_R_IFB1152704058:0	NC	0	0.1464656	0.7788748	0.1139225	0.2370516
rs1000031-123_B_F_IFB1135583872:0	NC	0.1418234	0.09989066	1.886752	0.1056218	-0.2568504
rs1000032-126_B_R_IFB1136145093:0	BB	0.384529	0.9843265	1.277473	1	0.1722209
rs10000388-126_B_F_IFB1135932472:0	AA	0.1695461	0.09100197	1.313618	0.08207574	-0.0548007
rs1000040-126_T_F_IFB1152704061:0	NC	0	0.1466142	1.192073	0.1114842	0.4565158
rs1000041-126_T_F_IFB1153889147:0	BB	0.8351063	0.9792455	1.47053	0.9974457	0.06689198
rs10000432-126_T_R_IFB1135756304:0	NC	0.0382568	0.5999213	0.911589	0.4233809	0.433604

Total number of rows: 370404

Table truncated, full table size 30841 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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