Cell Systems
Volume 8, Issue 4, 24 April 2019, Pages 352-357.e3
Journal home page for Cell Systems

Tool
exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling

https://doi.org/10.1016/j.cels.2019.03.004Get rights and content
Under a Creative Commons license
open access

Highlights

  • exceRpt processes and analyzes exRNA profiling data

  • exceRpt generates quality control metrics, RNA abundance estimates, and reports

  • A user-friendly, browser-based graphical interface is available

  • exceRpt processes all RNA-seq datasets in the exRNA Atlas

Summary

Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one’s confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.

Keywords

bioinformatics
exRNAs
RNA-seq
genomics
extracellular RNA
RNA sequencing
transcriptome
bioinformatics tool
pipeline

Cited by (0)

5

These authors contributed equally

6

Present address: Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA

7

Lead Contact