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Sample GSM1048134 Query DataSets for GSM1048134
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, 1035
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 5
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 1035.1_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 0.798095569472169
cg00001349 0.795750285275658
cg00001583 0.027791906193933
cg00002028 0.0443145697785203
cg00003202 0.0120799025960045
cg00003287 0.0593246907992745
cg00004121 0.42754898357255
cg00007036 0.974269830901713
cg00007898 0.0240052000322142
cg00008004 0.0947836917724117
cg00008647 0.0461093520998825
cg00009292 0.16402225169973
cg00009916 0.0147379995064622
cg00011717 0.900924494610429
cg00014168 0.765480052389134
cg00015286 0.767244249877346
cg00015930 0.973468485764816
cg00016238 0.944723691368923
cg00017221 0.0216446495088282
cg00017437 0.031817958753274

Total number of rows: 330168

Table truncated, full table size 9445 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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