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Sample GSM1048167 Query DataSets for GSM1048167
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 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: 2
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 B1057.2_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 0.87639426233275
cg00001349 0.814835575081114
cg00001583 0.0187058962909857
cg00002028 0.0562502840370568
cg00003202 0.0227122800509458
cg00003287 0.0485583853931489
cg00004121 0.56124731979852
cg00007036 0.959366657610251
cg00007898 0.0372368707909586
cg00008004 0.13285775255742
cg00008647 0.0521331523415137
cg00009292 0.144308831393435
cg00009916 0.0279391950416357
cg00011717 0.95144448523059
cg00014168 0.775760283434169
cg00015286 0.816961409546508
cg00015930 0.985644642094887
cg00016238 0.907835262602884
cg00017221 0.0134425227631795
cg00017437 0.0245118403655045

Total number of rows: 330168

Table truncated, full table size 9444 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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