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Sample GSM1048157 Query DataSets for GSM1048157
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1042
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 6
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 B1042.1_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 0.783546537312497
cg00001349 0.739701694644675
cg00001583 0.0427617044201031
cg00002028 0.0813352745976857
cg00003202 0.0160143987762615
cg00003287 0.0821521850433144
cg00004121 0.489684242240104
cg00007036 0.933051082643679
cg00007898 0.0292425714273976
cg00008004 0.0684072897314868
cg00008647 0.056528689134629
cg00009292 0.18104128873512
cg00009916 0.0178341123552311
cg00011717 0.9122325235114
cg00014168 0.802654200351879
cg00015286 0.787185235929322
cg00015930 0.964364804186181
cg00016238 0.836909184249528
cg00017221 0.047751007487742
cg00017437 0.0239731541098394

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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