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Sample GSM1048138 Query DataSets for GSM1048138
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, 2034
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: 13
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 2034.1_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 0.85740837914288
cg00001349 0.75309210075621
cg00001583 0.0232793983170746
cg00002028 0.0408487954115594
cg00003202 0.0177738004514885
cg00003287 0.0937393224386771
cg00004121 0.434877139392427
cg00007036 0.956585237304506
cg00007898 0.0230172179482505
cg00008004 0.052502777359568
cg00008647 0.045630428570899
cg00009292 0.166068681495816
cg00009916 0.0158274074287343
cg00011717 0.91006673335984
cg00014168 0.805052364434377
cg00015286 0.824006295868343
cg00015930 0.977223272661585
cg00016238 0.955631045541916
cg00017221 0.0328589929115087
cg00017437 0.031370694865357

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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