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Sample GSM1048181 Query DataSets for GSM1048181
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1126
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 12
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 B1126.2_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 0.800039816345813
cg00001349 0.809972356811188
cg00001583 0.0265744956207311
cg00002028 0.074972660622768
cg00003202 0.0150506424189498
cg00003287 0.0710401104217161
cg00004121 0.572118187089506
cg00007036 0.939457367412725
cg00007898 0.0323653996107657
cg00008004 0.0805844907170558
cg00008647 0.0659628283375032
cg00009292 0.144713781885201
cg00009916 0.0207653003951148
cg00011717 0.904789094796856
cg00014168 0.733171524356187
cg00015286 0.798437801023833
cg00015930 0.974068629857271
cg00016238 0.91231506354493
cg00017221 0.0250107798448307
cg00017437 0.0195586581895639

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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