Datasets:
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---
license: unknown
tags:
- biology
- rna
- genomics
configs:
- config_name: hepg2
data_files:
- split: train
path: eclip-hepg2.parquet
- config_name: k562
data_files:
- split: train
path: eclip-k562.parquet
---
# Overview
eCLIP is an experimental protocol which measures the in vivo binding sites of RNA-binding proteins (RBPs) across the transcriptome by coupling ultraviolet crosslinking, immunoprecipitation, and high-throughput sequencing. In this dataset, the eCLIP tracks have been reprocessed using [Peakhood](https://github.com/BackofenLab/Peakhood) to report the number of RBP-specific binding sites across two cell lines.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
# Data Format
Description of data columns:
- `target_{rbp}`: Number of binding sites in transcript for specific RBP.
- `cds`: Binary track which reports position of first nucleotide in each codon in CDS.
- `splice`: Binary track which reports position of the 3' end of each exon, indicating splice sites.
# Data Source
This dataset is generated using raw eCLIP data generated by the Yeo lab as part of the ENCODE project: https://www.encodeproject.org/eclip/. (See ENCODE [data use policy](https://www.encodeproject.org/help/citing-encode/))
Please attribute:
ENCODE paper: https://www.nature.com/articles/nature11247
eCLIP Protocol: https://www.nature.com/articles/nmeth.3810
Original dataset source: https://www.encodeproject.org/
Citations:
- The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). https://doi.org/10.1038/nature11247
- Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810 |