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Sample GSM1048160 Query DataSets for GSM1048160
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1046
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: 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_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 0.819808051119577
cg00001349 0.734172232152343
cg00001583 0.0165825732296574
cg00002028 0.0618465260563244
cg00003202 0.0112441452055498
cg00003287 0.094929268548138
cg00004121 0.608191006946775
cg00007036 0.979724505828462
cg00007898 0.0173816925033851
cg00008004 0.137329545612858
cg00008647 0.0696275431854169
cg00009292 0.229721451596001
cg00009916 0.0228762528151398
cg00011717 0.939523462492824
cg00014168 0.740251327201361
cg00015286 0.887061571211782
cg00015930 0.97053179271578
cg00016238 0.776407017156547
cg00017221 0.0431628370816975
cg00017437 0.0207797733205243

Total number of rows: 330168

Table truncated, full table size 9441 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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