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Sample GSM1048161 Query DataSets for GSM1048161
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1046
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: 0
sibship: 7
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 B1046.1_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 0.757503301155562
cg00001349 0.758397374447375
cg00001583 0.0162789998186859
cg00002028 0.0721772956613696
cg00003202 0.0249456158692622
cg00003287 0.059885069836832
cg00004121 0.584530269011325
cg00007036 0.968930474795087
cg00007898 0.0417688718735819
cg00008004 0.139364554898149
cg00008647 0.0766710964514858
cg00009292 0.153033403037185
cg00009916 0.0202208071001813
cg00011717 0.920261792683098
cg00014168 0.693966498793561
cg00015286 0.845502809035959
cg00015930 0.979157196962481
cg00016238 0.892778834210076
cg00017221 0.0187150203415177
cg00017437 0.0188972384496376

Total number of rows: 330168

Table truncated, full table size 9446 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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