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--- |
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license: unknown |
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tags: |
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- biology |
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- rna |
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- genomics |
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configs: |
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- config_name: hepg2 |
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data_files: |
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- split: train |
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path: eclip-hepg2.parquet |
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- config_name: k562 |
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data_files: |
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- split: train |
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path: eclip-k562.parquet |
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--- |
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# Overview |
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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. |
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This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench |
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# Data Format |
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Description of data columns: |
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- `target_{rbp}`: Number of binding sites in transcript for specific RBP. |
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- `cds`: Binary track which reports position of first nucleotide in each codon in CDS. |
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- `splice`: Binary track which reports position of the 3' end of each exon, indicating splice sites. |
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# Data Source |
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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/)) |
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Please attribute: |
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ENCODE paper: https://www.nature.com/articles/nature11247 |
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eCLIP Protocol: https://www.nature.com/articles/nmeth.3810 |
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Original dataset source: https://www.encodeproject.org/ |
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Citations: |
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- 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 |
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- 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 |
