Data from: RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy

Dataset

RoboCOP (Robotic Chromatin Occupancy Profile) is a state space model that incorporates chromatin accessibility data and nucleotide sequence to predict nucleosome positions and transcription factor binding sites. In this paper, we generated the binding profile of the yeast genome using MNase-seq data. We find that the binding profile changes when yeast cells are treated with cadmium for 60 mins. We compare the two binding profiles by running RoboCOP separately with the two MNase-seq data sets: one before cadmium treatment and one after 60 minutes of cadmium treatment. From RoboCOP output, we notice significant changes in the binding profile around the most up-regulated and down-regulated genes. We obtain the set of genes with most changes from the RNA-seq data for the same two time points as the MNase-seq data sets. The software published via GitHub as of 01/24/2020 is also available as a Zip file (RoboCOP-master_github.zip) with this data package.

Data Access

Duke Authors

Cited Authors

  • Mitra, S; MacAlpine, D; Zhong, J; Hartemink, A

Published Date

  • January 24, 2020

Digital Object Identifier (DOI)

  • 10.7924/r4hx1b43s