| Title |
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data / |
| Authors |
Derr, Alan ; Yang, Chaoxing ; Žilionis, Rapolas ; Sergushichev, Alexey ; Blodgett, David M ; Redick, Sambra ; Bortell, Rita ; Luban, Jeremy ; Harlan, David M ; Kadener, Sebastian ; Greiner, Dale L ; Klein, Allon ; Artyomov, Maxim N ; Garber, Manuel |
| DOI |
10.1101/gr.207902.116 |
| Full Text |
|
| Is Part of |
Genome research.. Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press. 2016, Vol. 26, Iss. 10, p. 1397-1410.. ISSN 1088-9051. eISSN 1549-5469 |
| Keywords [eng] |
gene-expression ; virus-infection ; high-throughput ; genome ; type-2 ; polyadenylation ; quantification ; proliferation ; amplification ; resolution |
| Abstract [eng] |
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 endsequencing 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. |
| Published |
Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press |
| Type |
Journal article |
| Language |
English |
| Publication date |
2016 |
