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Sample GSM1048165 Query DataSets for GSM1048165
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1057
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 8
twin: 1
Extracted molecule genomic DNA
Extraction protocol gDNA was purified from buccal swabs using phenol chloroform extraction.
Label Cy5 and Cy3
Label protocol Bisulphite conversion was carried out using the Methyl Xceed bisulphite kit as per the manufacturer's instructions.
Hybridization protocol Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 BeadChip using the standard llumina protocol.
Scan protocol Arrays were imaged using the BeadArray Reader using the standard recommended Illumina scanner setting.
Description B1057.1 _B
Data processing Data were preprocessed using the Bioconductor Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.
Submission date Dec 03, 2012
Last update date Mar 06, 2013
Contact name David Martino
Phone 0863191635
Organization name Telethon Kids Institute
Street address Perth Childrens Hospital, 15 Hospital Avenue
State/province Western Australia
ZIP/Postal code 6009
Country Australia
Platform ID GPL13534
Series (1)
GSE42700 Epigenome analysis of buccal cells from monozygotic and dizygotic twins

Data table header descriptions
VALUE Quantile-normalized average Beta

Data table
cg00000957 0.777553995370816
cg00001349 0.774560720387406
cg00001583 0.0261133718218732
cg00002028 0.0552308273281762
cg00003202 0.0182935682675644
cg00003287 0.088000569678371
cg00004121 0.541180821271717
cg00007036 0.914786605005436
cg00007898 0.0473432294328422
cg00008004 0.0659585510509488
cg00008647 0.0565384191449122
cg00009292 0.15140236875408
cg00009916 0.00877454592784873
cg00011717 0.912858264917257
cg00014168 0.786340541781178
cg00015286 0.792234138846504
cg00015930 0.983643256628543
cg00016238 0.927016617858178
cg00017221 0.0401015289404966
cg00017437 0.0240345807840714

Total number of rows: 330168

Table truncated, full table size 9443 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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