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Sample GSM1048175 Query DataSets for GSM1048175
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1072
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 10
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 B1072.2_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 0.815539796287073
cg00001349 0.778678410111885
cg00001583 0.04492795337094
cg00002028 0.0600818511462769
cg00003202 0.0210472863691087
cg00003287 0.0678708756376894
cg00004121 0.50974087871805
cg00007036 0.921599363387761
cg00007898 0.0238746007683583
cg00008004 0.0938527167470597
cg00008647 0.0659565195712725
cg00009292 0.171589568660373
cg00009916 0.0186560024544824
cg00011717 0.906306332653448
cg00014168 0.728342350983079
cg00015286 0.747614229747728
cg00015930 0.972472160305734
cg00016238 0.898911762309674
cg00017221 0.0360285315888789
cg00017437 0.0598427095804099

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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