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Sample GSM1048144 Query DataSets for GSM1048144
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 3014
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: 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_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 0.819500929938246
cg00001349 0.808025410960628
cg00001583 0.0168480500873215
cg00002028 0.0368098389046188
cg00003202 0.0172291191238065
cg00003287 0.087432142783981
cg00004121 0.539554295351718
cg00007036 0.948269297096269
cg00007898 0.0215553197706391
cg00008004 0.0875067084895605
cg00008647 0.0325528557809518
cg00009292 0.160665093314308
cg00009916 0.0205429911770596
cg00011717 0.947714733594154
cg00014168 0.738572693003571
cg00015286 0.829542936093433
cg00015930 0.975320750669023
cg00016238 0.860292835093752
cg00017221 0.0263168426860056
cg00017437 0.0404699345677357

Total number of rows: 330168

Table truncated, full table size 9440 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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