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Sample GSM539196

Query DataSets for GSM539196

Status

Public on Dec 07, 2010

Title

Normal N6_sty

Sample type

genomic

Source name

whole blood DNA extraction

Organism

Homo sapiens

Characteristics

sample type: normal reference
tissue: blood
disease state: normal

Extracted molecule

genomic DNA

Extraction protocol

QiaAmp DNA Blood Kit

Label

Biotin

Label protocol

As per manufacturer (Affymetrix)

Hybridization protocol

DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

Scan protocol

The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

Description

Hybridized to 250K_Sty

Data processing

The CEL-Files were analyzed using the BRLMM-algorithm to produce genotype calls, stored in the corresponding CHP-Files.
CEL- and CHP-Format by Affymetrix

Submission date

Apr 29, 2010

Last update date

Dec 07, 2010

Contact name

Rene Scholtysik

E-mail(s)

rene.scholtysik@uni-due.de

Organization name

University Hospital Essen

Department

IFZ

Street address

Virchowstrasse 173

City

Essen

ZIP/Postal code

45127

Country

Germany

Platform ID

GPL3720

Series (1)

GSE21597

Affymetrix SNP array data for Burkitt lymphoma samples

Data table header descriptions
ID_REF
VALUE	Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1	Relative allele signal for the data in the first probe group
RAS2	Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF	VALUE	CONFIDENCE	RAS1	RAS2	P-VALUE AA	P-VALUE AB	P-VALUE BB	P-VALUE NO CALL
AFFX-5Q-123	No Call	437.5	0	0	0	0	0	0
AFFX-5Q-456	No Call	513.5	0	0	0	0	0	0
AFFX-5Q-789	No Call	793.5	0	0	0	0	0	0
AFFX-5Q-ABC	No Call	1259	0	0	0	0	0	0
AFFX-barcodeA	No Call	230.5	0	0	0	0	0	0
AFFX-barcodeB	No Call	374.5	0	0	0	0	0	0
AFFX-barcodeC	No Call	109	0	0	0	0	0	0
AFFX-barcodeD	No Call	106.5	0	0	0	0	0	0
AFFX-barcodeE	No Call	143.5	0	0	0	0	0	0
AFFX-barcodeF	No Call	147.5	0	0	0	0	0	0
AFFX-barcodeG	No Call	138	0	0	0	0	0	0
AFFX-barcodeH	No Call	211.5	0	0	0	0	0	0
AFFX-barcodeI	No Call	182	0	0	0	0	0	0
AFFX-barcodeJ	No Call	157	0	0	0	0	0	0
AFFX-barcodeK	No Call	138.5	0	0	0	0	0	0
AFFX-barcodeL	No Call	152.5	0	0	0	0	0	0
AFFX-barcodeM	No Call	159.5	0	0	0	0	0	0
AFFX-barcodeN	No Call	214.5	0	0	0	0	0	0
AFFX-barcodeO	No Call	137.5	0	0	0	0	0	0
AFFX-barcodeP	No Call	200.5	0	0	0	0	0	0

Total number of rows: 238378

Table truncated, full table size 18484 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM539196_N6_sty.CEL.gz	26.5 Mb	(ftp)(http)	CEL
GSM539196_Normal_N6.chp.gz	3.8 Mb	(ftp)(http)	CHP
Processed data included within Sample table
Processed data provided as supplementary file