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Sample GSM1048151 Query DataSets for GSM1048151
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1024
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: 0
sibship: 3
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 B1024.1_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 0.884788847822023
cg00001349 0.776143387545107
cg00001583 0.0335429980304139
cg00002028 0.0598453108782616
cg00003202 0.0163450408951569
cg00003287 0.123003693905287
cg00004121 0.545038817716224
cg00007036 0.962680697167429
cg00007898 0.0372746176099
cg00008004 0.0794448307704232
cg00008647 0.0560210805655775
cg00009292 0.138858042382569
cg00009916 0.0144598471050827
cg00011717 0.93487317265868
cg00014168 0.692237020849952
cg00015286 0.736529939214942
cg00015930 0.978610849430455
cg00016238 0.934903451935474
cg00017221 0.035379586206205
cg00017437 0.0232268991576299

Total number of rows: 330168

Table truncated, full table size 9445 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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