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Sample GSM1048156 Query DataSets for GSM1048156
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1042
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 6
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 B1042.1_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 0.836859727775024
cg00001349 0.793157510934358
cg00001583 0.0405480005579921
cg00002028 0.0659737316923738
cg00003202 0.0197732855135682
cg00003287 0.0749478411047013
cg00004121 0.48456494628427
cg00007036 0.93740482238179
cg00007898 0.0381298642742217
cg00008004 0.118435564221609
cg00008647 0.0685042109097002
cg00009292 0.222735869447331
cg00009916 0.0214327484617528
cg00011717 0.913708582456888
cg00014168 0.856742348304283
cg00015286 0.794758270153277
cg00015930 0.96153567079587
cg00016238 0.774614273515297
cg00017221 0.0385593130729665
cg00017437 0.0274080865922326

Total number of rows: 330168

Table truncated, full table size 9438 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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