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Sample GSM1048136 Query DataSets for GSM1048136
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 1035
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: 5
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 1035.2_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 0.874012552574871
cg00001349 0.612148084600926
cg00001583 0.053401071268447
cg00002028 0.0534417765786463
cg00003202 0.0113583336179025
cg00003287 0.128051581001929
cg00004121 0.355221413746489
cg00007036 0.852978390243885
cg00007898 0.0266371678610585
cg00008004 0.0730995537739944
cg00008647 0.0536368726629486
cg00009292 0.185394590569303
cg00009916 0.0135907476661938
cg00011717 0.927089670431769
cg00014168 0.860459962555682
cg00015286 0.729140892505141
cg00015930 0.971624279485057
cg00016238 0.93022688865485
cg00017221 0.0309386888122338
cg00017437 0.0434278287798111

Total number of rows: 330168

Table truncated, full table size 9444 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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