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Sample GSM1048145 Query DataSets for GSM1048145
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1016
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: 1
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 B1016.1_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 0.812778353875744
cg00001349 0.78482649717212
cg00001583 0.015504942543531
cg00002028 0.0518618865702227
cg00003202 0.0131454363390154
cg00003287 0.0692953348975191
cg00004121 0.617511738974193
cg00007036 0.96148570675775
cg00007898 0.0514371658805872
cg00008004 0.181323831265129
cg00008647 0.0763904958001728
cg00009292 0.206172785883284
cg00009916 0.0760970660412992
cg00011717 0.924051686662644
cg00014168 0.802260686507762
cg00015286 0.830789932883079
cg00015930 0.976278329395752
cg00016238 0.863099466000095
cg00017221 0.050231737786827
cg00017437 0.0243700454857362

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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