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Series GSE90735 Query DataSets for GSE90735
Status Public on Oct 19, 2017
Title Sodium arsenite effects on DNA methylation in zebrafish embryos.
Organism Danio rerio
Experiment type Methylation profiling by high throughput sequencing
Summary There is a need to develop biomarkers in alternative testing models predictive for chemically induced chronic disease in humans, preferably describing key events and their relationships in an adverse outcome pathway analysis. Epigenetic modifications, and particularly DNA methylation effects, have been implicated as a major event in susceptibility to develop chronic disease. Arsenic exposure affects large populations around the world through drinking water and industrial activities. We sought to identify epigenetic markers of arsenic exposure. We analyzed the effect of sodium arsenite on DNA methylation in Danio rerio (zebrafish) embryos using unbiased methylation profiling by high throughput sequencing.
 
Overall design Pools of zebrafish embryos exposed to 0.1 mM and 1 mM sodium arsenite and non-exposed controls were analyzed in quadruplicates by DNA methylation profiling using DREAM (Digital Restriction Enzyme Analysis of Methylation). In short, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.
 
Contributor(s) van der Ven LM, Jelinek J, Hodemaekers HM, Zwart EP, Ruiter S, van den Brandhof E, Bakker F, Issa JJ, Pennings JA, Luijten M
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Submission date Dec 01, 2016
Last update date May 15, 2019
Contact name Jaroslav Jelinek
E-mail(s) jjelinek@coriell.org
Phone 8567579739
Organization name Coriell Institute for Medical Research
Department Research Labs
Street address 403 Haddon Avenue
City Camden
State/province NJ
ZIP/Postal code 08103
Country USA
 
Platforms (1)
GPL18413 Illumina HiSeq 2500 (Danio rerio)
Samples (12)
GSM2411595 Control 1
GSM2411596 Control 2
GSM2411597 Control 3
Relations
BioProject PRJNA355643
SRA SRP094418

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Supplementary file Size Download File type/resource
GSE90735_RAW.tar 6.7 Mb (http)(custom) TAR (of TXT)
GSE90735_methylation_table.txt.gz 49.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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