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Sample GSM1048183 Query DataSets for GSM1048183
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B3006
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 14
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 B3006.1_B
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 0.816595645596858
cg00001349 0.765289094414531
cg00001583 0.0318619558349543
cg00002028 0.0465593629669832
cg00003202 0.0214719047162562
cg00003287 0.101518102790254
cg00004121 0.597809529034917
cg00007036 0.939260937940313
cg00007898 0.0348024782667029
cg00008004 0.0511904286198607
cg00008647 0.0608659644914807
cg00009292 0.154743568490386
cg00009916 0.0261403376882914
cg00011717 0.926234299835351
cg00014168 0.759918654795881
cg00015286 0.809647136104258
cg00015930 0.973531685187299
cg00016238 0.898135031328459
cg00017221 0.0396971585763966
cg00017437 0.0215410693625036

Total number of rows: 330168

Table truncated, full table size 9432 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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