This track displays genome-wide, strand-specific transcription levels from 1,054 individual ENCODE total RNA-seq experiments. The data capture both coding and non-coding RNAs profiled across all phases of the ENCODE project. The signal shown is derived from the reads per million (RPM) of uniquely mapped reads on each genomic strand. The data are processed following the ENCODE bulk RNA-seq pipeline.
Each subtrack represents a single RNA-seq experiment in a specific biosample, with separate signal tracks for the plus and minus strands. These datasets provide the underlying experimental signals used to generate the corresponding layered summary tracks. Additional datasets measuring transcription levels are available at the ENCODE portal.
Subtracks are organized by strand (plus and minus strand views). Click a specific biosample type and organ/tissue combination to view available datasets. Subtracks can be further filtered by life stage of the biosample. Each track is colored based on the organ/tissue of origin.
The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored in bigWig files that can be downloaded from our download server. The data may also be explored interactively using our REST API. The original data files are also available from the ENCODE portal. Clicking any accession in the track's configuration table links directly to the corresponding file details page on the ENCODE portal.
These files may also be locally explored using our tool bigWigToWig,
which can be compiled from the source code or downloaded as a precompiled
binary for your system. Instructions for downloading source code and binaries can be found
here.
The tool can also be used to obtain data confined to a given range, e.g.,
bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2021/05/24/2b7c3f15-8fca-4159-95e3-abe926455192/ENCFF046IVV.bigWig stdout
Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Alexander Hoffmann (UCLA), Barbara Wold (Caltech), Manuel Garber (UMass), Michael Snyder (Stanford), Ross Hardison (PennState), and Thomas Gingeras (CSHL).
The data were further processed for visualization through a collaborative effort between the Weng lab and the Moore lab at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. PMID: 32728249; PMC: PMC7410828
Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. Nature. 2026 January 7. PMID: 39763870; PMC: PMC11703161