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Sample GSM1048169 Query DataSets for GSM1048169
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1058
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: 9
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 B1058.1_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 0.850455936594871
cg00001349 0.761663968083388
cg00001583 0.03295408064708
cg00002028 0.0569732037222099
cg00003202 0.0249017768587805
cg00003287 0.0685728203658077
cg00004121 0.54569578043307
cg00007036 0.931455517021286
cg00007898 0.0371271480706716
cg00008004 0.117313515067096
cg00008647 0.0677244992656182
cg00009292 0.202536613941461
cg00009916 0.0156039291109361
cg00011717 0.916153734551852
cg00014168 0.64186294899757
cg00015286 0.799418707471955
cg00015930 0.952433044016268
cg00016238 0.939117628704377
cg00017221 0.0428904726203084
cg00017437 0.00635013366831267

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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