Dataset Details

Title: Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes

Accession Number: Not Available

Link to Dataset: https://github.com/annebozack/SRP_arsenic_DNAm_metaanalysis

Repository: GitHub

Data Type(s): Code

Organism(s): Homo sapiens

Summary: This repository contains the necessary scripts to reproduce the analysis of Bozack et al.'s "Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes". The organization of the repository is as follows: The bangladesh-study folder contains the scripts and results associated with the Bangladesh DNAm studies. The chile-study directory is made up of subdirectories containing the code and results associated with the buccal cell and the PBMC DNAm analyses. It also holds a directory with notebooks assessing the within-participant buccal-PBMC sample similarities, and a directory with a notebook of descriptive statistics used to create Table 1 in the accompanying paper. The DMR-meta-analysis folder contains the DMR-meta-analysis.Rmd notebook, which details the meta-analysis procedure and summarized the results output by comb-p. The helper-scripts directory contains multiple helper files used to perform the analyses described in the paper.

Publication(s) associated with this dataset:

• Bozack AK, Boileau P, Wei L, Hubbard AE, Sille FC, Ferreccio Readi C, Acevedo J, Hou L, Ilievski V, Steinmaus CM, Smith MT, Navas-Acien A, Gamble MV, Cardenas A. 2021. Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes. Environ Health 20:79. doi:10.1186/s12940-021-00754-7 PMID:34243768 PMCID:PMC8272372

Project(s) associated with this dataset:

• Columbia University: Nutritional Influences on Blood Arsenic, Arsenic Methylation and Cognitive Function in Children
• University of California-Berkeley: Data Science and Laboratory Core