ChIP and Chips: Introducing the WormPharm for correlative studies employing pharmacology and genome-wide analyses in C. elegans

Jung H Doh; Andrew B Moore; İrem Çelen; Michael T Moore; Chandram R Sabanayagam

doi:10.14440/jbm.2016.109

ChIP and Chips: Introducing the WormPharm for correlative studies employing pharmacology and genome-wide analyses in C. elegans

J Biol Methods. 2016 Jun 10;3(2):e44. doi: 10.14440/jbm.2016.109. eCollection 2016.

Authors

Jung H Doh¹, Andrew B Moore², İrem Çelen³, Michael T Moore¹, Chandram R Sabanayagam¹

Affiliations

¹ University of Delaware, Delaware Biotechnology Institute, Newark, DE, USA.
² University of Delaware, Department of Biological Sciences, Newark, DE, USA.
³ University of Delaware, Center for Bioinformatics and Computational Biology, Newark, DE, USA.

Abstract

We present the WormPharm, an automated microfluidic platform that utilizes an axenic medium to culture C. elegans. The WormPharm is capable of sustaining C. elegans for extended periods, while recording worm development and growth with high temporal resolution ranging from seconds to minutes over several days to months. We demonstrate the utility of the device to monitor C. elegans growth in the presence of varying doses of nicotine and alcohol. Furthermore, we show that C. elegans cultured in the WormPharm are amendable for high-throughput genomic assays, i.e. chromatin-immunoprecipitation followed by next generation sequencing, and confirm that nematodes grown in monoxenic and axenic cultures exhibit genetic modifications that correlate with observed phenotypes. The WormPharm is a powerful tool for analyzing the effects of chemical, nutritional and environmental variations on organism level responses in conjunction with genome-wide changes in C. elegans.

Keywords: C. elegans; CeHR; ChIP-seq; WormPharm; Wormchip; axenic; growth kinetics.