title: End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.
abstract: 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 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct β-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.
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Derr
authors.affiliation: Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Chaoxing
authors.initials: C
authors.lastname: Yang
authors.affiliation: Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Biotechnology, Vilnius University, LT 02241 Vilnius, Lithuania.
authors.forename: Rapolas
authors.initials: R
authors.lastname: Zilionis
authors.affiliation: Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Sergushichev
authors.affiliation: Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Blodgett
authors.affiliation: Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Sambra
authors.initials: S
authors.lastname: Redick
authors.affiliation: Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Rita
authors.initials: R
authors.lastname: Bortell
authors.affiliation: Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Luban
authors.affiliation: Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Harlan
authors.affiliation: Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kadener
authors.affiliation: Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Dale L
authors.initials: DL
authors.lastname: Greiner
authors.affiliation: Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Allon
authors.initials: A
authors.lastname: Klein
authors.affiliation: Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA.
authors.forename: Maxim N
authors.initials: MN
authors.lastname: Artyomov
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
authors.forename: Manuel
authors.identifier: 0000-0001-8732-1293
authors.initials: M
authors.lastname: Garber
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D003713:Dendritic Cells / Q000166:cytology / Q000378:metabolism; D015723:Gene Library; D007515:Islets of Langerhans / Q000166:cytology* / Q000378:metabolism; D044085:Microfluidics / Q000379:methods; D051381:Rats; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards; D059010:Single-Cell Analysis / Q000379:methods* / Q000592:standards; D059467:Transcriptome