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Sample GSM1048146 Query DataSets for GSM1048146
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1016
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: 1
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 B1016.1_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 0.839821040614064
cg00001349 0.852535226643383
cg00001583 0.02383456659225
cg00002028 0.0744143556462082
cg00003202 0.0255379881734658
cg00003287 0.0879926143086194
cg00004121 0.593329667781976
cg00007036 0.965001057831909
cg00007898 0.0181529193617352
cg00008004 0.0770448969819425
cg00008647 0.0693104201985354
cg00009292 0.141412805005847
cg00009916 0.0191356787026282
cg00011717 0.919582595644808
cg00014168 0.794583996338007
cg00015286 0.844290897860758
cg00015930 0.970765119976121
cg00016238 0.802186760436173
cg00017221 0.0359966681886687
cg00017437 0.017613577307209

Total number of rows: 330168

Table truncated, full table size 9447 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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