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Sample GSM1860879 Query DataSets for GSM1860879
Status Public on Aug 26, 2015
Title peripheral T cells-ice storm-405
Sample type genomic
 
Source name peripheral T cells/ice storm/405
Organism Homo sapiens
Characteristics storm32: 8
iesr_ts: 0
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 -0.352160296306777 0.104993899751185
cg00212031 -0.914608508769355 0.371824177166413
cg00213748 9.96434086779242 0.895006100248815
cg00214611 2.64909283814087 0.615223878742182
cg00455876 -2.72973402493513 5.93797559678144e-07
cg01707559 -1.30544816106401 1.11022302462516e-16
cg02004872 -4.10433665981474 0.0292545300255924
cg02011394 -0.117183539370339 0.321579481073476
cg02050847 -9.96434086779242 0.700705891341283
cg02233190 -3.7135910857924 0.0157935701128857
cg02494853 -5.03280827216928 0
cg02839557 -9.96434086779242 0.863657251923459
cg02842889 -9.96434086779242 0.855051429509539
cg03052502 0.191577600985896 0.139343624547825
cg03155755 1.0607540310791 0.283561003966952
cg03244189 -1.1073835353736 0.00343122262068951
cg03443143 -0.505423735735949 0.068739828076957
cg03683899 -9.96434086779242 0.916496263608508
cg03695421 -1.55915331437155 0.175610645502842
cg03706273 -6.38495214751828 0

Total number of rows: 485577

Table truncated, full table size 14465 Kbytes.




Supplementary file Size Download File type/resource
GSM1860879_8667053044_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1860879_8667053044_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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