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Sample GSM1048185 Query DataSets for GSM1048185
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 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: 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 B3006.2_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 0.817552967282047
cg00001349 0.738616626296585
cg00001583 0.0367422883848361
cg00002028 0.0540623716960222
cg00003202 0.0279290526704183
cg00003287 0.0729676262274165
cg00004121 0.601426837754389
cg00007036 0.95297742204516
cg00007898 0.0432556171345437
cg00008004 0.0691871670913641
cg00008647 0.055000843434513
cg00009292 0.165614752540868
cg00009916 0.0391107355626481
cg00011717 0.926713889778687
cg00014168 0.701299074254092
cg00015286 0.749220188018391
cg00015930 0.967773208013176
cg00016238 0.87906964609026
cg00017221 0.0708527137086162
cg00017437 0.0265696156241587

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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