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Sample GSM1048173 Query DataSets for GSM1048173
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1072
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 10
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 B1072.1_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 0.850385924442762
cg00001349 0.738296575432332
cg00001583 0.0376025526231754
cg00002028 0.0754520623174773
cg00003202 0.023870926323785
cg00003287 0.0840593254563449
cg00004121 0.521704473276981
cg00007036 0.959628169802909
cg00007898 0.0238514004180235
cg00008004 0.0989322160035045
cg00008647 0.0774551305747578
cg00009292 0.140183687956138
cg00009916 0.0191407792118977
cg00011717 0.923349139795346
cg00014168 0.672360021123758
cg00015286 0.808992003645056
cg00015930 0.96940591097118
cg00016238 0.788148483468171
cg00017221 0.0377073735155113
cg00017437 0.024718427665428

Total number of rows: 330168

Table truncated, full table size 9439 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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