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Sample GSM1301366 Query DataSets for GSM1301366
Status Public on Apr 02, 2014
Title UC Sample 199
Sample type RNA
 
Source name Umbilical cord
Organism Homo sapiens
Characteristics gender: Male
ethnicity: Chinese
batch: 1
Extracted molecule genomic DNA
Extraction protocol A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment, additionof TNES lysis buffer and Proteinase K.
Label Cy3 and Cy5
Label protocol Standard Illumina Infinium HD assay protocol
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Data processing Background subtraction was performed in GenomeStudio then data was exported. Probes were filtered for detection p-value <0.05 and NBEADS>3 in R. Data was then loaded into Arraystudio version 6 (Omicsoft). All technical replicates were combined after sample QC. Data were normalised amongst samples using quantile normalization and subjected to Combat to removed batch effect.
 
Submission date Jan 03, 2014
Last update date Apr 02, 2014
Contact name Dennis Wang
Organization name Singapore Institute for Clinical Sciences
Street address 30 Medical Drive
City Singapore
ZIP/Postal code 117609
Country Singapore
 
Platform ID GPL13534
Series (2)
GSE53816 The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes (methylomes)
GSE54446 The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes

Data table header descriptions
ID_REF
VALUE Normalized Average Beta

Data table
ID_REF VALUE
cg00000769 0.0592738
cg00000957 0.820409
cg00001245 0.0102402
cg00001261 0.43275
cg00001793 0.769226
cg00002033 0.0230576
cg00002116 0.00581412
cg00002719 3.55E-05
cg00002769 0.727702
cg00002809 0.893074
cg00002837 0.279164
cg00003202 0.0120954
cg00003287 0.1786
cg00003298 0.0102087
cg00003625 0.257201
cg00004067 0.933355
cg00004082 0.0483471
cg00004883 0.962145
cg00004979 0.937006
cg00005083 0.850937

Total number of rows: 485577

Table truncated, full table size 8093 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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