GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1048135 Query DataSets for GSM1048135
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, 1035
Sample type genomic
Source name Buccal cheek swab, MZ, 18 months
Organism Homo sapiens
Characteristics gender: female
age: 18 months
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 5
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 1035.2_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 0.837387605889634
cg00001349 0.775014282478071
cg00001583 0.027243280275079
cg00002028 0.0494556813139496
cg00003202 0.0147267863970542
cg00003287 0.0917798322237939
cg00004121 0.492710754788342
cg00007036 0.950200646485024
cg00007898 0.0290612968710542
cg00008004 0.138815847787328
cg00008647 0.0484611851121292
cg00009292 0.155712670521856
cg00009916 0.043193763271495
cg00011717 0.950144716287968
cg00014168 0.861231134611603
cg00015286 0.781499937626268
cg00015930 0.975661331242012
cg00016238 0.917029002833526
cg00017221 0.0361773830303241
cg00017437 0.0298959763923972

Total number of rows: 330168

Table truncated, full table size 9438 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap