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Sample GSM539144

Query DataSets for GSM539144

Status

Public on Dec 07, 2010

Title

Normal N3_nsp

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_Nsp

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

GPL3718

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	451.5	0	0	0	0	0	0
AFFX-5Q-456	No Call	474.5	0	0	0	0	0	0
AFFX-5Q-789	No Call	824	0	0	0	0	0	0
AFFX-5Q-ABC	No Call	1214	0	0	0	0	0	0
AFFX-barcodeA	No Call	206.5	0	0	0	0	0	0
AFFX-barcodeB	No Call	407.5	0	0	0	0	0	0
AFFX-barcodeC	No Call	103.5	0	0	0	0	0	0
AFFX-barcodeD	No Call	94.5	0	0	0	0	0	0
AFFX-barcodeE	No Call	147.5	0	0	0	0	0	0
AFFX-barcodeF	No Call	144.5	0	0	0	0	0	0
AFFX-barcodeG	No Call	147	0	0	0	0	0	0
AFFX-barcodeH	No Call	176.5	0	0	0	0	0	0
AFFX-barcodeI	No Call	219	0	0	0	0	0	0
AFFX-barcodeJ	No Call	132.5	0	0	0	0	0	0
AFFX-barcodeK	No Call	130	0	0	0	0	0	0
AFFX-barcodeL	No Call	129	0	0	0	0	0	0
AFFX-barcodeM	No Call	123.5	0	0	0	0	0	0
AFFX-barcodeN	No Call	188.5	0	0	0	0	0	0
AFFX-barcodeO	No Call	122.5	0	0	0	0	0	0
AFFX-barcodeP	No Call	169.5	0	0	0	0	0	0

Total number of rows: 262338

Table truncated, full table size 20295 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM539144_N3_nsp.CEL.gz	26.0 Mb	(ftp)(http)	CEL
GSM539144_Normal_N3_nsp.chp.gz	4.1 Mb	(ftp)(http)	CHP
Processed data included within Sample table
Processed data provided as supplementary file