GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1366829

Query DataSets for GSM1366829

Status

Public on Sep 01, 2014

Title

P008

Sample type

genomic

Source name

blood

Organism

Characteristics

trio: P008
person: child

Extracted molecule

genomic DNA

Extraction protocol

Total RNA extraction from frozen placental tissue was performed using mirVana™ miRNA Isolation Kit (Ambion®, Life Technologies™), according to the manufacturer’s instructions.

Label

Cy3, Cy5

Label protocol

Illumina Infinium HD Assay Kit

Hybridization protocol

standard Illumina protocol

Scan protocol

Illumina HiScan scanner, analysis was done using Genome Studio 2010 Genotyping module 1.8.4

Data processing

SNP calling was performed with GenomeStudio (2010.3) using 95% call rate criterion.

Submission date

Apr 10, 2014

Last update date

Sep 01, 2014

Contact name

Tauno Metsalu

Organization name

University of Tartu

Street address

Liivi 2

City

Tartu

ZIP/Postal code

50409

Country

Estonia

Platform ID

Series (2)

GSE56685	Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping)
GSE56781	Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta

Data table header descriptions
ID_REF
VALUE	log2 ratio
Allele1 - Top
Allele2 - Top
GC Score
Allele1 - Forward
Allele2 - Forward
B Allele Freq
GT Score

Data table
ID_REF	VALUE	Allele1 - Top	Allele2 - Top	GC Score	Allele1 - Forward	Allele2 - Forward	B Allele Freq	GT Score
exm-IND1-200449980-0_M_R_1990486447	-0.3246	I	I	0.75	I	I	0.9915	0.7601
exm-IND1-201453487-0_M_R_1990486448	-0.0042	I	I	0.8892	I	I	0.9995	0.8991
exm-IND1-85310248-0_P_F_1990486624	0.1997	I	I	0.8345	I	I	0	0.8554
exm-IND10-102817747-0_P_F_1990486569	-0.0378	D	D	0.8071	D	D	1	0.7945
exm-IND10-18329639-0_M_R_1990486442	-0.0054	D	D	0.4111	D	D	0	0.8219
exm-IND10-27476467-0_M_R_1990486443	-0.0485	I	I	0.8761	I	I	1	0.8433
exm-IND10-27727540-0_M_R_1990486444	0.1395	D	D	0.9519	D	D	1	0.9193
exm-IND10-74560589-0_P_F_1990486573	0.0854	D	D	0.9304	D	D	0	0.8936
exm-IND11-102094357-0_P_F_1990486575	0.0312	D	D	0.8054	D	D	0	0.8352
exm-IND11-60867390-0_M_R_1990486445	-0.1279	I	I	0.8305	I	I	0.9666	0.8525
exm-IND11-73463127-0_P_F_1990486580	-0.2655	I	I	0.8781	I	I	0.0047	0.8894
exm-IND12-4584372-0_P_F_1990486581	-0.0498	I	I	0.7442	I	I	0.0093	0.7966
exm-IND12-46829523-0_M_R_1990486450	0.0349	I	I	0.8088	I	I	0	0.8375
exm-IND12-49036005-0_P_F_1990486582	0.1783	I	I	0.8854	I	I	0	0.8957
exm-IND12-51232970-0_P_F_1990486584	-0.0016	I	I	0.8358	I	I	1	0.8563
exm-IND12-54361914-0_M_R_1990486452	0.1068	I	I	0.7001	I	I	0.001	0.7709
exm-IND12-67380833-0_P_F_1990486586	0.1657	D	D	0.529	D	D	0	0.9172
exm-IND12-83947680-0_M_R_1990486453	0.2359	I	I	0.7911	I	I	0	0.8257
exm-IND12-8887191-0_M_R_1990486455	-0.1695	I	I	0.9177	I	I	0.9963	0.8804
exm-IND13-47565698-0_P_F_1990486590	0.1435	I	I	0.8982	I	I	0	0.9073

Total number of rows: 242901

Table truncated, full table size 14447 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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