The Encyclopedia of DNA elements (ENCODE): data portal update

Abstract

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

U2 AF 65 assemblies drive sequence‐specific splice site recognition

“…We found a significant positive correlation of "Splicing Changes" upon knockdown of CAPERa and U2AF 65 with the DSPY scores ( Fig 4F, Spearman rho = 0.40, P = 1.6E-03 and rho = 0.33, P = 8.8E-03, respectively). To generalize these observations, we performed similar analyses using available RNA-Seq data for K562 [43], HeLa [44], MCF7 [42], and HEK293T [45] cells. We aligned reads to our library of sequences corresponding to 5,629 cassette exon inclusions and exclusions.…”

The how and why of lncRNA function: An innate immune perspective

“…In contrast, if a researcher is studying a mouse candidate lncRNA, the Mouse Cell Atlas (MCA) [99], as well as Tabula Muris [100] are excellent tools to assess specificity in cellular expression, as well as differential splicing isoforms amongst differentiated cell types. Additional websites for mouse and human expression datasets can be found at the ENCODE project [101], the European Bioinformatics Institute Expression and the FANTOM projects [102]. These sites are filled with raw and analyzed data sets from either single cell or bulk RNA sequencing from primary cells, tissues or immortalized cells ready to use to determine the statistical significance of expression for any annotated lncRNA candidate.…”

“…Identifying the types of epigenetic histone marks will add additional layers of understanding if the candidate is active, poised, silenced or an enhancer. Many publicly available datasets provide this information outlined in Tables 1 and 2. While the examples we outlined here are immune focused there is a vast array of additional primary and immortalized cell line for every histone mark available through the easily accessible ENCODE database [101].…”

Hit and Run Transcriptional Repressors Are Difficult to Catch in the Act

“…We examined RNA‐seq and GATA1 ChIP‐seq data arising from G1E‐ER4 cells generated as part of the Encyclopedia of DNA Elements (ENCODE) project . Full details of the datasets used and methodology are available in the Supporting Information.…”