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Sample GSM1048147 Query DataSets for GSM1048147
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1016
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 0
sibship: 1
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 B1016.2_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 0.875811068555184
cg00001349 0.80713611503617
cg00001583 0.0230163654675764
cg00002028 0.0653512138015491
cg00003202 0.0113374541558323
cg00003287 0.0498973428312144
cg00004121 0.612541523256902
cg00007036 0.946154054300965
cg00007898 0.0464003610160205
cg00008004 0.0610593763521314
cg00008647 0.061736132341857
cg00009292 0.176635077466583
cg00009916 0.0222901170503698
cg00011717 0.927270586510815
cg00014168 0.771463377790276
cg00015286 0.82702708476485
cg00015930 0.975295168609369
cg00016238 0.838821660123769
cg00017221 0.0441040885592598
cg00017437 0.024139706234084

Total number of rows: 330168

Table truncated, full table size 9443 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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