- 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 ... [Read More]
- Total Size
- 11 files (2.79 GB)
- Data Citation
- Mitra, S., Zhong, J., MacAlpine, D., Hartemink, A., MacAlpine, H. (2020). Data from: RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy. Duke Research Data Repository. https://doi.org/10.7924/r4hx1b43s
- DOI
- 10.7924/r4hx1b43s
- Publication Date
- January 24, 2020
- ARK
- ark:/87924/r4hx1b43s
- Contributor
- Affiliation
- Publisher
- Type
- Related Materials
- Title
- Data from: RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy
- Repository
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README.txt | 2020-01-24 | Download | |
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getMidpointCounts.py | 2020-01-24 | Download | |
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MNase_CD_0mins.bam | 2020-01-24 | Download | |
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MNase_CD_0mins.bam.bai | 2020-01-24 | Download | |
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MNase_CD_60mins.bam | 2020-01-24 | Download | |
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MNase_CD_60mins.bam.bai | 2020-01-24 | Download | |
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RNA_CD_0mins.bam | 2020-01-24 | Download | |
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RNA_CD_0mins.bam.bai | 2020-01-24 | Download | |
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RNA_CD_60mins.bam | 2020-01-24 | Download | |
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RNA_CD_60mins.bam.bai | 2020-01-24 | Download |