GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2443853

Query DataSets for GSM2443853

Status

Public on Jan 04, 2020

Title

Godoberi1032

Sample type

genomic

Source name

cheek swab

Organism

Characteristics

population: Godoberi
village: Godoberi
region: Daghestan
gender: Female

Extracted molecule

genomic DNA

Extraction protocol

Extraction of genomic DNA from cheek swab was performed using standard extraction protocols.

Label

biotin

Label protocol

Standard Illumina procedures.

Hybridization protocol

Standard Illumina procedures.

Scan protocol

Standard Illumina procedures.

Description

Genomic DNA extracted from cheek swab was genotyped using Illumina HumanOmniExpress-24 v1.0 BeadChip platform.

Data processing

Illumina GenomeStudio Software has been used to analyze the data. GenomeStudio Genotyping Module Version is 1.9.4.

Submission date

Jan 04, 2017

Last update date

Jan 04, 2020

Contact name

Tatiana M. Karafet

E-mail(s)

tkarafet@email.arizona.edu

Phone

520-626-0404

Organization name

University of Arizona

Department

ARL

Lab

Michael Hammer's Research Group

Street address

BSW #246, 1041 E Lowell Str.

City

Tucson

State/province

AZ

ZIP/Postal code

85721

Country

USA

Platform ID

Series (1)

Genetic variation in four highland populations in the context of broader genetic diversity in Daghestan.

Data table header descriptions
ID_REF	IlmnID
VALUE	Genotype: AA,AB,BB,or NC (no call)
Theta
R
B_Allele_Freq
GC_Score
Log_R_Ratio
Genotype

Data table
ID_REF	VALUE	Theta	R	B_Allele_Freq	GC_Score	Log_R_Ratio	Genotype
rs1000000-131_B_F_1894802339	AB	0.413	2.304	0.5151	0.7942	-0.0298	AG
rs1000002-131_T_F_1889659641	AA	0.016	1.116	0.0010	0.8844	-0.0347	TT
rs10000023-131_B_F_1908645866	BB	0.975	1.663	1.0000	0.8082	-0.0493	GG
rs1000003-131_B_R_1891325219	AA	0.040	1.852	0.0000	0.7431	-0.1200	AA
rs10000030-131_B_R_1891267789	AB	0.659	0.620	0.4788	0.8397	0.0111	AG
rs10000037-131_B_R_1891342139	AB	0.418	1.421	0.4488	0.9088	0.1140	AG
rs10000041-131_T_R_1893970874	AB	0.490	1.125	0.5134	0.9066	-0.2178	TG
rs10000042-131_T_R_1895028553	BB	0.981	1.017	1.0000	0.7871	0.0896	CC
rs10000049-131_T_F_1893954592	AA	0.048	1.243	0.0131	0.4568	-0.0012	AA
rs1000007-131_T_F_1891267790	BB	0.979	1.104	1.0000	0.8475	0.2537	CC
rs10000073-131_T_R_1895048370	AA	0.003	0.967	0.0000	0.8805	-0.0231	TT
rs10000081-131_B_F_1895064663	AA	0.033	0.828	0.0000	0.8697	-0.2637	TT
rs10000092-131_T_R_1911627639	AA	0.000	0.774	0.0000	0.8353	0.0413	TT
rs10000105-131_T_F_1893943453	BB	0.963	1.065	0.9990	0.4874	0.0020	GG
rs10000119-131_T_R_1893947293	BB	0.957	1.247	0.9916	0.8404	-0.0024	CC
rs10000124-131_B_R_1908800786	BB	0.978	1.540	1.0000	0.8184	0.0229	CC
rs10000154-131_T_F_1893949661	AB	0.531	1.123	0.4954	0.9105	0.0661	AG
rs1000016-131_B_R_1891268428	AA	0.016	1.584	0.0000	0.8294	-0.0011	AA
rs10000160-131_T_F_1895138379	BB	0.965	0.991	1.0000	0.7916	-0.2788	GG
rs10000169-131_T_R_1891213580	AA	0.020	0.832	0.0000	0.9043	0.0315	TT

Total number of rows: 708595

Table truncated, full table size 47482 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM2443853_200641710015_R07C01_Grn.idat.gz	5.0 Mb	(ftp)(http)	IDAT
GSM2443853_200641710015_R07C01_Red.idat.gz	5.1 Mb	(ftp)(http)	IDAT
Processed data provided as supplementary file
Processed data are available on Series record

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