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Sample GSM1048164 Query DataSets for GSM1048164
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1057
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: 8
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 B1057.1_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 0.819512868929708
cg00001349 0.789334808427187
cg00001583 0.0216424675918538
cg00002028 0.064087900261461
cg00003202 0.0195756217362238
cg00003287 0.0780511219330447
cg00004121 0.556766951360124
cg00007036 0.957206834089918
cg00007898 0.0370407301263647
cg00008004 0.0842717319799313
cg00008647 0.0884691647120635
cg00009292 0.175907286723959
cg00009916 0.0115878511467402
cg00011717 0.870846244603112
cg00014168 0.814444186706503
cg00015286 0.763786996092002
cg00015930 0.983925483101227
cg00016238 0.943333246726547
cg00017221 0.0117140393174022
cg00017437 0.0325357892824205

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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