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Sample GSM1860908 Query DataSets for GSM1860908
Status Public on Aug 26, 2015
Title peripheral T cells-ice storm-1316
Sample type genomic
 
Source name peripheral T cells/ice storm/1316
Organism Homo sapiens
Characteristics storm32: 9
iesr_ts: 2
Sex: F
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 -0.202816882999687 0.515227407138804
cg00212031 1.36257007938471 0.879163255272187
cg00213748 -1.07623558582708 0.143972369980351
cg00214611 9.96434086779242 0.913354934296359
cg00455876 -2.58818640159544 1.2315175057509e-07
cg01707559 -1.49274834615107 0
cg02004872 -2.52253329644774 0.000296493809288867
cg02011394 -1 0.387308702661742
cg02050847 0.144705011453035 0.0850856687953149
cg02233190 -2.17978624995859 5.94059055127882e-05
cg02494853 -5.1140357783702 0
cg02839557 9.96434086779242 0.864512459062826
cg02842889 0.752072486556414 0.414734126126789
cg03052502 0.449971289388231 0.207685182165475
cg03155755 0.726981505593584 0.0261442002320381
cg03244189 -0.683526335204746 1.10753178850231e-08
cg03443143 -0.43195088221519 0.046491911334419
cg03683899 -0.0232073911613248 0.188292409145722
cg03695421 -0.138605238229507 0.001259546870645
cg03706273 -5.10907855484367 0

Total number of rows: 485577

Table truncated, full table size 14466 Kbytes.




Supplementary file Size Download File type/resource
GSM1860908_8667053096_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1860908_8667053096_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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