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Sample GSM1048154 Query DataSets for GSM1048154
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1032
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: female
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 4
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 B1032.2_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 0.859897735584525
cg00001349 0.898596770034561
cg00001583 0.0377654883140981
cg00002028 0.0645185311850651
cg00003202 0.0189797042211761
cg00003287 0.0707391728454272
cg00004121 0.502443156399452
cg00007036 0.962862666096637
cg00007898 0.0480008400562264
cg00008004 0.0574538516417075
cg00008647 0.0584706581147238
cg00009292 0.173711653237253
cg00009916 0.0201884361257464
cg00011717 0.900996002249988
cg00014168 0.644804452234095
cg00015286 0.69729182647148
cg00015930 0.968531981762851
cg00016238 0.789216012610898
cg00017221 0.0234768071385019
cg00017437 0.0215948231352681

Total number of rows: 330168

Table truncated, full table size 9440 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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