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Sample GSM1048142 Query DataSets for GSM1048142
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, 3014
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: 15
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 3014.1_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 0.780154759924462
cg00001349 0.791110688758211
cg00001583 0.0307929582393625
cg00002028 0.0350134408942418
cg00003202 0.0191804279238778
cg00003287 0.0895282835417082
cg00004121 0.563068531838886
cg00007036 0.944383476637664
cg00007898 0.033348119331864
cg00008004 0.0648800498445965
cg00008647 0.0496950411096046
cg00009292 0.17253512460206
cg00009916 0.0116559633057152
cg00011717 0.926197901234636
cg00014168 0.71272003015453
cg00015286 0.826867272425713
cg00015930 0.976152215617506
cg00016238 0.902935316586817
cg00017221 0.0261464439956026
cg00017437 0.0319665672550226

Total number of rows: 330168

Table truncated, full table size 9442 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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