Overview of the ENCODE RNA Trackhub

The ENCODE RNA Trackhub contains signals and peaks produced by the ENCODE Consortium for genome-wide assays related to RNA and RNA-associated protein factors (mostly RNA-binding proteins or RBPs), produced till Feb 1, 2019. Included assays profile RNA expression (RNA-seq), transcription start site activity (RAMPAGE and CAGE), microRNA expression (microRNA-seq), binding by RBPs (eCLIP), and RNA expression after knocking down an RBP with shRNAs (shRNA + RNA-seq).  All data included in this trackhub were produced by ENCODE uniform processing pipelines for the respective assays and are publicly available at the ENCODE Portal. In each dataset, peaks are the genomic regions with significantly high signals. The peaks in this trackhub constitute a component of the ground-level of the ENCODE Encyclopedia. The hub contains data mapped to both the human genome (versions GRCh38 and hg19) and the mouse genome (version mm10) and is updated periodically as more data are produced by ENCODE.  To facilitate navigation, we have organized the hub in three ways: (1) all data are grouped by assay and further sub-grouped by biosample for each assay, in the “CAGE”, “eCLIP (by biosample)”, “RAMPAGE”, “microRNA-seq”, “RNA-seq (by cellular compartment)”, “RNA-seq (by protocol)”, and “shRNA + RNA-seq (by biosample)” composite tracks; (2) eCLIP and shRNA + RNA-seq experiments are grouped by the targeted RBP in the “eCLIP (by target)” and “shRNA + RNA-seq (by target)” composite tracks; (3) data from all assays are grouped by tissue ontology, defined with metadata obtained from the ENCODE Portal, in the "Experiments by Ontology" composite track.

Note:

A related trackhub named “ENCODE DNA Trackhub” contains signals and peaks produced by the ENCODE Consortium for genome-wide assays related to DNA and chromatin-associated factors produced till Feb 1, 2019.

The “ENCODE DNA Trackhub” and the “ENCODE RNA Trackhub” contain the raw data and output from the ENCODE uniform processing pipelines for individual experiments. Annotations from integrated analyses of multiple experiments, such as a Registry of candidate cis-regulatory elements (cCREs) and other integrated-level components of the ENCODE Encyclopedia are available in a separate, associated trackhub named “ENCODE Integrative Annotation Trackhub”.

Available assays

The following assays have data available. See ENCODE data processing pipeline description for more information.

• RNA-seq (hg19, GRCh38, mm10): profiles RNA expression. Plus and minus strand signals are available for all experiments. Both total RNA-seq and Poly-A RNA-seq have been performed, with some datasets in a particular cellular compartment (e.g., nuclear, cytosol, cytosol, etc.) as well as RNA-seq following shRNA-knockdown of an RBP. Expression profiles, expressed in tags per million sequencing reads (TPM) and fragment per kilobase of transcript per million sequencing reads (FPKM) for individual genes, are available at the visualizer SCREEN.
• RAMPAGE (GRCh38, hg19): profiles the activities of transcription start sites (TSS). Plus and minus strand signal and RAMPAGE peaks (calls of transcription start sites or TSS) are available for all experiments. Visualization of the activity profiles of individual TSSs across biosamples is also available at SCREEN.
• CAGE (hg19, GRCh38): Maps the 5 ́ ends of mRNAs. Available data types include plus and minus strand signals and CAGE peaks (TSS calls).
• eCLIP-seq (hg19, GRCh38): profiles the binding sites of RNA binding proteins (RBPs). Available data types include signals and peaks. See the eCLIP computational pipeline overview for more information.

Acknowledgments

Thanks to the ENCODE Consortium, the ENCODE production laboratories, and the ENCODE Data Coordination Center for generating and processing the datasets used here. The ENCODE accession numbers of the constituent datasets are available from the peak details page. Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) developed this trackhub. Special thanks to Kate Rosenbloom and Jim Kent at UCSC for guidance developing this trackhub.

References

ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, et al. 2020. "Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes." Nature 583 (7818): 699–710.

Contact

Please contact henry.pratt@umassmed.edu with any questions or comments about this trackhub.