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Series GSE157111 Query DataSets for GSE157111
Status Public on Oct 27, 2021
Title Genome-wide DNA methylation profiles of Arsenic exposed subjects through drinking water in Pakistan
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Ground water Arsenic (As) toxicity is a global problem and millions of people are exposed to elevated levels (more than WHO advised maximum limit of 10µg/L) through drinking water. The exposure is associated with various cancerous and non-cancerous diseases. It may alter DNA methylation profiles of inviduals and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also has reported elevated ground water As levels in various investigations since 2005. However, a very limited biomonitoring studies have been conducted in this context while no study reports molecular changes associated with drinking water As exposure in Pakistan. Within this context, the present study aimed to investigate genome-wide DNA methylation profiles of the exposed subjects in two districts of Punjab Province Pakistan, i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. Genome-wide DNA methylation profiles were obtained using MeDIP in combination with NimbleGen 2.1M Deluxe Promotor arrays.
Overall design Freshly taken blood samples were collected form the respective exposure groups and transported in dry ice to Department of Toxicogenomics Maastricht University, The Netherlands for further analysis. DNA was isolated from buffy coats for performing global DNA methylation analysis using Methylated DNA immunoprecipitation (MeDIP-CHIP) on NimbleGen 2.1M Deluxe Promotors arrays (Roche, NimbleGen).
Contributor(s) Rehman MY, Kleinjans JC, Briedé JJ, van Herwijnen M, Krauskopf J, Jennen DG, Malik RN
Citation(s) 34619179
Submission date Aug 29, 2020
Last update date Oct 29, 2021
Contact name Danyel Jennen
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 40
City Maastricht
ZIP/Postal code 6229ER
Country Netherlands
Platforms (1)
GPL16284 NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100929_HG19_Deluxe_Prom_Meth_HX1]
Samples (57)
GSM4753201 Low Arsenic exposed subject SM16
GSM4753202 Low Arsenic exposed subject SM18
GSM4753203 Low Arsenic exposed subject SM19
BioProject PRJNA660163

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE157111_CpG_sites_arsenic_Pakistan.txt.gz 961.1 Mb (ftp)(http) TXT
GSE157111_RAW.tar 4.9 Gb (http)(custom) TAR (of PAIR)
Processed data are available on Series record

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