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Sample GSM1108086

Query DataSets for GSM1108086

Status

Public on Mar 28, 2013

Title

CD14 4

Sample type

genomic

Source name

CD14

Organism

Homo sapiens

Characteristics

gender: NA

Extracted molecule

genomic DNA

Extraction protocol

DNA from Buccal cells was extracted using the Gentra Puregene Buccal cell kit, USA. CD14 and CD34 cells were extracted using Qiagen QIAamp DNA Blood Mini Kit, Sperm was extracted by Qiagen QIAamp DNA Mini Kit, Placenta (Catalog number D1234200 from Biochain, USA) and Pancreas (Catalog number D1234188 from Biochain, USA) were commercial samples

Label

Cy5 and Cy3

Label protocol

Standard Illumina Protocol

Hybridization protocol

Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

Scan protocol

Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

Description

Normal

Data processing

BeadStudio software, Custom R scripts for normalisation provided in supplementary of paper.

Submission date

Mar 27, 2013

Last update date

Mar 28, 2013

Contact name

Robert Lowe

Organization name

QMUL

Department

Blizard Institute

Street address

4 Newark Street

City

London

ZIP/Postal code

E1 2AT

Country

United Kingdom

Platform ID

GPL13534

Series (2)

GSE45529	Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies
GSE46573	Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Illumina tiling]

Data table header descriptions
ID_REF
VALUE	normalized (Quantile normalised on a per probe type and colour channel basis) Average Beta
Detection Pval

Data table
ID_REF	VALUE	Detection Pval
cg13332474	0.0422867045731227	0
cg00651829	0.0272911681834047	0
cg17027195	0.0254451363915446	0
cg22461835	0.218275077942523	0
cg03050183	0.146246899612724	0
cg01989731	0.822996205927643	0
cg04244851	0.900168164879798	0
cg19669385	0.948815318580914	0
cg04244855	0.897277979461246	0
cg17689707	0.052506398428665	0
cg06671842	0.0909164450466666	0
cg02434381	0.106391628663344	0
cg05777492	0.0597968189379047	0
cg25970726	0.649411982590981	0
cg23340034	0.892315262552305	0
cg25428494	0.409420829855729	0
cg20024403	0.146507068651293	0
cg01686522	0.958860407048806	0
cg10855395	0.293964590924833	0
cg26361540	0.0567445292947443	0

Total number of rows: 441946

Table truncated, full table size 13475 Kbytes.

Supplementary data files not provided

Processed data included within Sample table