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

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.

RoboCOP（Robotic Chromatin Occupancy Profile）是一款整合染色质可及性数据与核苷酸序列的状态空间模型，可用于预测核小体位置与转录因子结合位点。本研究利用微球菌核酸酶测序（MNase-seq）数据生成了酵母基因组的结合谱。研究发现，当酵母细胞经镉处理60分钟后，其结合谱会发生改变。我们分别使用两组MNase-seq数据集（一组为镉处理前样本，另一组为镉处理60分钟后样本）独立运行RoboCOP，以对比两组结合谱的差异。从RoboCOP的输出结果中，我们观察到在上调与下调幅度最大的基因周边区域，结合谱存在显著变化。我们还从与MNase-seq数据集对应时间点的RNA测序（RNA-seq）数据中，获取了表达变化最显著的基因集合。本软件已于2020年1月24日通过GitHub发布，同时随本数据包一并提供压缩包版本（RoboCOP-master_github.zip）。