GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM539210

Query DataSets for GSM539210

Status

Public on Dec 07, 2010

Title

Normal RefDNAc

Sample type

genomic

Source name

Reference DNA provided by Affymetrix

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	337	0	0	0	0	0	0
AFFX-5Q-456	No Call	319	0	0	0	0	0	0
AFFX-5Q-789	No Call	831.5	0	0	0	0	0	0
AFFX-5Q-ABC	No Call	1025	0	0	0	0	0	0
AFFX-barcodeA	No Call	137	0	0	0	0	0	0
AFFX-barcodeB	No Call	288.5	0	0	0	0	0	0
AFFX-barcodeC	No Call	92.5	0	0	0	0	0	0
AFFX-barcodeD	No Call	85.5	0	0	0	0	0	0
AFFX-barcodeE	No Call	127.5	0	0	0	0	0	0
AFFX-barcodeF	No Call	112.5	0	0	0	0	0	0
AFFX-barcodeG	No Call	131	0	0	0	0	0	0
AFFX-barcodeH	No Call	133.5	0	0	0	0	0	0
AFFX-barcodeI	No Call	170.5	0	0	0	0	0	0
AFFX-barcodeJ	No Call	122	0	0	0	0	0	0
AFFX-barcodeK	No Call	95.5	0	0	0	0	0	0
AFFX-barcodeL	No Call	128.5	0	0	0	0	0	0
AFFX-barcodeM	No Call	117	0	0	0	0	0	0
AFFX-barcodeN	No Call	172	0	0	0	0	0	0
AFFX-barcodeO	No Call	111.5	0	0	0	0	0	0
AFFX-barcodeP	No Call	141.5	0	0	0	0	0	0

Total number of rows: 238378

Table truncated, full table size 18581 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM539210_Normal_RefDNAc.chp.gz	3.8 Mb	(ftp)(http)	CHP
GSM539210_RefDNAc_sty.CEL.gz	25.5 Mb	(ftp)(http)	CEL
Processed data included within Sample table
Processed data provided as supplementary file