https://github.com/danko-lab/chro-seq_paper_data
https://github.com/danko-lab/chro-seq_paper_data
Last synced: 10 months ago
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- Host: GitHub
- URL: https://github.com/danko-lab/chro-seq_paper_data
- Owner: Danko-Lab
- Created: 2024-04-17T16:08:29.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-04-17T16:41:21.000Z (about 2 years ago)
- Last Synced: 2024-04-17T17:33:34.548Z (about 2 years ago)
- Language: R
- Size: 10.2 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
ChRO-seq_paper_data
========
* This repository contains the TRE data reported in the ChRO-seq paper "Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme" in Nature Genetics (https://www.nature.com/articles/s41588-018-0244-3).
GBM_TRE
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This directory contains TREs called by dREG.HD under the stringent criterion. They reprent active enhancers and promoters identified using ChRO-seq data. (The coordinate is hg19).
23samples.tsTRE
-------
This directory contains bed files of tumor-associated TREs (taTRE).
* bed.files : taTRE identified in each primary GBM/pdx sample by excluding DHS sites from normal adult brain samples from TREs in GBM_TRE. This corresponds to the statistics reported in supplementary table 4 of the ChRO-seq paper.
* bad.regions: blacklisted regions reported by ENCODE project.
* all.merged.bed: taTREs merged across samples in bed.files followed by excluding the set in bad.regions.