Comprehensive Characterization of Single-cell Full-length Isoforms in Human and Mouse with Long-read Sequencing

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2021 Nov 12

PMID 34763716

Citations 86

Authors

Luyi Tian

Jafar S Jabbari

Rachel Thijssen

Quentin Gouil

Shanika L Amarasinghe

Oliver Voogd

Hasaru Kariyawasam

Mei R M Du

Jakob Schuster

Changqing Wang

Shian Su

Xueyi Dong

Charity W Law

Alexis Lucattini

Yair David Joseph Prawer

Coralina Collar-Fernandez

Jin D Chung

Timur Naim

Audrey Chan

Chi Hai Ly

Gordon S Lynch

James G Ryall

Casey J A Anttila

Hongke Peng

Mary Ann Anderson

Christoffer Flensburg

Ian Majewski

Andrew W Roberts

David C S Huang

Michael B Clark

Matthew E Ritchie

Affiliations

Soon will be listed here.

Abstract

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.

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