GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM539194

Query DataSets for GSM539194

Status

Public on Dec 07, 2010

Title

Normal N4_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	547	0	0	0	0	0	0
AFFX-5Q-456	No Call	503	0	0	0	0	0	0
AFFX-5Q-789	No Call	935	0	0	0	0	0	0
AFFX-5Q-ABC	No Call	1451	0	0	0	0	0	0
AFFX-barcodeA	No Call	235.5	0	0	0	0	0	0
AFFX-barcodeB	No Call	470.5	0	0	0	0	0	0
AFFX-barcodeC	No Call	105.5	0	0	0	0	0	0
AFFX-barcodeD	No Call	106	0	0	0	0	0	0
AFFX-barcodeE	No Call	157.5	0	0	0	0	0	0
AFFX-barcodeF	No Call	147	0	0	0	0	0	0
AFFX-barcodeG	No Call	128	0	0	0	0	0	0
AFFX-barcodeH	No Call	176.5	0	0	0	0	0	0
AFFX-barcodeI	No Call	206.5	0	0	0	0	0	0
AFFX-barcodeJ	No Call	178	0	0	0	0	0	0
AFFX-barcodeK	No Call	150.5	0	0	0	0	0	0
AFFX-barcodeL	No Call	193.5	0	0	0	0	0	0
AFFX-barcodeM	No Call	175.5	0	0	0	0	0	0
AFFX-barcodeN	No Call	240.5	0	0	0	0	0	0
AFFX-barcodeO	No Call	154.5	0	0	0	0	0	0
AFFX-barcodeP	No Call	191.5	0	0	0	0	0	0

Total number of rows: 238378

Table truncated, full table size 18406 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM539194_N4_sty.CEL.gz	26.3 Mb	(ftp)(http)	CEL
GSM539194_Normal_N4.chp.gz	3.8 Mb	(ftp)(http)	CHP
Processed data included within Sample table
Processed data provided as supplementary file