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Sample GSM1048170 Query DataSets for GSM1048170
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1058
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: 9
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 B1058.2_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 0.854792931310538
cg00001349 0.83380316953545
cg00001583 0.0306497464317999
cg00002028 0.0468501372702625
cg00003202 0.0175726833647177
cg00003287 0.161231970306943
cg00004121 0.567336640719513
cg00007036 0.955595211656928
cg00007898 0.0287803778697346
cg00008004 0.161518507782988
cg00008647 0.0615882203388296
cg00009292 0.136362970853731
cg00009916 0.0245964754815693
cg00011717 0.924358677856787
cg00014168 0.738179906589107
cg00015286 0.795174354604768
cg00015930 0.962211570998445
cg00016238 0.882012363174185
cg00017221 0.0432349160578852
cg00017437 0.0397123805776241

Total number of rows: 330168

Table truncated, full table size 9435 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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