PRO-cap, in the CoPRO form described by Tome et al., permeabilizes cells and runs a nuclear run-on reaction with biotinylated NTPs, which RNA polymerase incorporates into the nascent transcripts it is actively making. Biotinylated RNAs are captured on streptavidin beads, selected for a 5' cap so that only transcripts still carrying their original start are kept, then reverse transcribed and paired-end sequenced. The 5' end of the second read marks the base at which transcription started, and the read's strand gives the strand of initiation. The six experiments here were produced by the Yu and Lis labs at Cornell University and processed through the ENCODE PRO-cap pipeline, which maps reads, removes PCR duplicates using unique molecular identifiers, and writes -single-base plus and minus strand signal for the uniquely mapping reads. +single-base plus and minus strand signal for the uniquely mapping reads. These +experiments are part of the ENCODE 4 nascent transcriptome survey described in +Shah et al.
The signal files were downloaded from the ENCODE portal, taking for each experiment only the plus and minus strand signal of unique reads files belonging to that experiment's default analysis, which drops files superseded by a later reprocessing. The experiments are ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR098LLB, ENCSR261KBX and ENCSR799DGV for A673, Caco-2, Calu3, HUVEC, K562 and MCF10A respectively, and are linked from the Experiment column of the table on this page. ENCODE releases PRO-cap signal per replicate and, for MCF10A, per sequencing run, and publishes no pooled file, so the files were summed at UCSC to give one track per cell line per strand: two files for A673, Caco-2, Calu3 and K562, one for HUVEC, which has a single released replicate, and four for MCF10A. This is the same merge the ProCapNet models were trained on. Minus strand signal is negative as released by ENCODE and is kept that way. Total signal is conserved exactly by the summing. The steps are recorded in the makeDoc and the scripts are in the kent source tree, including the manifest recording exactly -which ENCODE files went into each track. +target="_blank">the kent source tree, including +proCapNetEncodeFiles.tsv, which records exactly which ENCODE file +accessions went into each track.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our -API, track=encode4ProCap. +API. The API returns one +bigWig at a time, so name a single strand of one cell line rather than the +container, for example track=encode4ProCap_K562_procap_pos.
The Files column of the table on this page links each cell line's bigWigs directly, so a single file can be fetched without working out its path.
For automated download and analysis, the genome annotation is stored in bigWig files that can be downloaded from our download server. The files are named for the cell line, the ENCODE experiment accession and the strand, for example K562.ENCSR261KBX.pos.bw and K562.ENCSR261KBX.neg.bw. Individual regions or the whole genome annotation can be obtained using our tool bigWigToBedGraph, which @@ -115,30 +120,44 @@ ENCODE portal under the experiment accessions listed above.
PRO-cap data was generated as part of ENCODE by Sagar Shah and the Yu and Lis labs at Cornell University. Thanks to the ENCODE Consortium and the ENCODE production laboratories for making the data available.
+Shah SR, Chen Y, Leung AK, Navarro PVC, Paramo MI, Gupta J, Gurumurthy A, Fite RF, Weimer AK, +Cochran K et al. + +The nascent transcriptome delineates the regulatory landscape in human health and disease. +bioRxiv. 2026 Jun 9;. +DOI: 10.1101/2025.09.24.676871; PMID: 41040139; PMC: PMC12485982 +
+ + +Tome JM, Tippens ND, Lis JT. Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers. Nat Genet. 2018 Nov;50(11):1533-1541. DOI: 10.1038/s41588-018-0234-5; PMID: 30349116; PMC: PMC6422046