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Sample GSM1860898 Query DataSets for GSM1860898
Status Public on Aug 26, 2015
Title peripheral T cells-ice storm-826
Sample type genomic
 
Source name peripheral T cells/ice storm/826
Organism Homo sapiens
Characteristics storm32: 11
iesr_ts: 9
Sex: M
tissue: T cell
Extracted molecule genomic DNA
Extraction protocol T cells were isolated from the PBMCs by immunomagnetic positive selection using CD3 dynabeads (Dynal). DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturers protocol. Genomic DNA was quantified using Picogreen protocol (Quant-iT PicoGreen dsDNA Products, Invitrogen) and read on SpectraMAX GeminiXS Spectrophotometer. Bisulfite conversion was performed with 250 ng of genomic DNA using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer's instructions.
Label Cy5 and Cy3
Label protocol Standard Illumina Infinium Assay Protocol
 
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.
Scan protocol Arrays were scanned using the Illumina iScan Reader using standard recommended Illumina scanner settings.
Data processing Extracted microarray intensities were preprocessed and normalized using the 'minfi' Bioconductor R package according to the Illumina Genome Studio protocol--background correction followed by normalization to control probes.
 
Submission date Aug 25, 2015
Last update date Aug 26, 2015
Contact name Moshe Szyf
E-mail(s) moshe.szyf@mcgill.ca
Organization name McGill University
Department Pharmacology
Street address McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309
City Montreal
State/province Quebec
ZIP/Postal code H3G 1Y6
Country Canada
 
Platform ID GPL13534
Series (1)
GSE72354 DNA methylation signatures triggered by prenatal maternal stress exposure to a natural disaster: Project Ice Storm

Data table header descriptions
ID_REF
VALUE Normalized probe intensities combined into methylation estimates (methylated signal/methylated signal + unmethylated signal) followed by logit (base 2) transformation.
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00050873 3.93598350712885 0
cg00212031 -3.58707690326468 0
cg00213748 9.96434086779242 0
cg00214611 -9.96434086779242 0
cg00455876 1.99969353265081 0
cg01707559 -3.72428646009546 0
cg02004872 -9.96434086779242 0
cg02011394 7.24211214094378 0
cg02050847 8.68468119688893 0
cg02233190 -3.29387237846652 0
cg02494853 -6.07653766737546 0
cg02839557 -4.8675407887382 0
cg02842889 -7.34389230040419 0
cg03052502 9.96434086779242 0
cg03155755 4.70611036453209 0
cg03244189 -4.24193361890468 0
cg03443143 4.27014263909994 0
cg03683899 -6.24236399937356 0
cg03695421 1.39845894604412 0
cg03706273 -5.37851162325373 0

Total number of rows: 485577

Table truncated, full table size 14457 Kbytes.




Supplementary file Size Download File type/resource
GSM1860898_8667053054_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1860898_8667053054_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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