Datasets:

morrislab
/

eclip

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 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)

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