UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; Diabetes Center of Excellence; Department of Medicine

Publication Date


Document Type

Article Postprint


Bioinformatics | Computational Biology | Genomics


RNA-seq protocols that focus on transcript termini are well-suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1,000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified 9 distinct cell types, three distinct beta-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single cell RNA end-sequencing.


UMCCTS funding

Rights and Permissions

This manuscript is Open Access. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at

DOI of Published Version



Genome Res. 2016 Jul 28. pii: gr.207902.116. Link to article on publisher's site

Journal/Book/Conference Title

Genome research


The version of the article available for download is the authors' final, peer-reviewed accepted manuscript as prepared for publication in Genome Research.

Related Resources

Link to Article in PubMed

PubMed ID


Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License



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