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Sample GSM1048148 Query DataSets for GSM1048148
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1022
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: 1
sibship: 2
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 B1022.1_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 0.773378982896092
cg00001349 0.782431319981104
cg00001583 0.0296162478506153
cg00002028 0.0597863147517563
cg00003202 0.0145688960652262
cg00003287 0.0367966598859994
cg00004121 0.560546691910442
cg00007036 0.975633844982732
cg00007898 0.0331542224236721
cg00008004 0.0819856330103542
cg00008647 0.0609893638441633
cg00009292 0.133480331139873
cg00009916 0.0255731494192395
cg00011717 0.920508574143298
cg00014168 0.781459421387906
cg00015286 0.852754446797078
cg00015930 0.967056597320474
cg00016238 0.779968337488847
cg00017221 0.027988593613935
cg00017437 0.0192917775550551

Total number of rows: 330168

Table truncated, full table size 9440 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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