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Sample GSM1048162 Query DataSets for GSM1048162
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1046
Sample type genomic
Source name Buccal cheek swab, MZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 0
sibship: 7
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 B1046.2_18m
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 0.835002974887645
cg00001349 0.824310646172031
cg00001583 0.031191754106875
cg00002028 0.0618874314444446
cg00003202 0.0158676436603817
cg00003287 0.046510324802605
cg00004121 0.570701222957062
cg00007036 0.959468980306767
cg00007898 0.0343634707289758
cg00008004 0.112014183340755
cg00008647 0.0741810551782214
cg00009292 0.181919083042735
cg00009916 0.0460426763805192
cg00011717 0.946375163264637
cg00014168 0.752978182464046
cg00015286 0.864547841382174
cg00015930 0.96808592104363
cg00016238 0.827288390554171
cg00017221 0.0381396393881291
cg00017437 0.0205963714288028

Total number of rows: 330168

Table truncated, full table size 9439 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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