Description

This track displays genome-wide transcription levels of coding and non-coding RNAs measured by total RNA-seq from ENCODE experiments. The signal represents reads per million (RPM) of uniquely mapped reads, shown separately for the plus and minus genomic strands. Each subtrack corresponds to an organ or tissue average of individual RNA-seq experiments. These datasets provide a broad view of transcriptional activity across the genome. Additional datasets measuring transcription levels are available at the ENCODE portal.

This track displays strand-specific total RNA-seq signals averaged across biosamples from the same organ or tissue. Two versions of each subtrack are available:

• Tissues and Primary Cells Only: Restricts to total RNA-seq data from tissues and primary cells, focusing on biosamples that more closely reflect in vivo cell states and developmental contexts.
• All Biosamples: Includes total RNA-seq data from all biosample types -- tissues, primary cells, cell lines, in vitro differentiated cells, and organoids -- providing a comprehensive view of transcription across diverse biological systems.

In both versions, RNA-seq signal is averaged across biosamples within the same organ/tissue category and displayed using a transparent overlay. For organs or tissues with only tissue or primary cell experiments, a single subtrack is shown because the two versions would be identical. For organs or tissues with only experiments from cell lines, in vitro differentiated cells, or organoids, a single all-biosample subtrack is shown. For organs or tissues that include both types, both versions are provided.

Available Organs and Tissues

Each organ or tissue is represented by two subtracks: one for the plus genomic strand and one for the minus strand. Subtracks prefixed with "All" include data from all biosample types (tissues, primary cells, cell lines, in vitro differentiated cells, and organoids), while subtracks without the prefix are restricted to tissues and primary cells only.

Display Conventions and Configuration

This track uses a transparent overlay to visualize data from multiple organs or tissues within the same vertical space. For each organ or tissue, signals from all associated experiments were averaged to generate the displayed track. Each organ or tissue is assigned a distinct color following the ENCODE color mapping convention, selected to be light and saturated to maintain clarity when overlaid. Initially, each layered track displays an overlay of five representative organs: blood, brain, kidney, liver, and muscle. Clicking on the track opens a details page where you can view and select organs or tissues. Subtracks can be further filtered by strandedness (+ strand or - strand) and life stage of the biosample.

Data Access

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.

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://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/regulation/organAve/adiposePlus.bw stdout

Credits

Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Barbara Wold (Caltech) 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.

References

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