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Sample GSM1048143 Query DataSets for GSM1048143
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, 3014
Sample type genomic
Source name Buccal cheek swab, MZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 15
twin: 2
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 3014.2_18M
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 0.848047436778707
cg00001349 0.852224311117925
cg00001583 0.0367044377081014
cg00002028 0.0392405093742464
cg00003202 0.0145389260610775
cg00003287 0.111415850073684
cg00004121 0.708183767094264
cg00007036 0.911997016911427
cg00007898 0.0205346448920342
cg00008004 0.166277878567712
cg00008647 0.0581090899130078
cg00009292 0.213975824557486
cg00009916 0.0393298131365767
cg00011717 0.964248651281852
cg00014168 0.870581871877856
cg00015286 0.831097830331618
cg00015930 0.966862508709349
cg00016238 0.90826947057991
cg00017221 0.0285837084528499
cg00017437 0.0390335520234244

Total number of rows: 330168

Table truncated, full table size 9437 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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