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Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

by Peng, Hongke , Amarasinghe, Shanika L. , Su, Shian , Ly, Chi Hai , Majewski, Ian , Tian, Luyi , Law, Charity W. , Roberts, Andrew W. , Lynch, Gordon S. , Chan, Audrey , Lucattini, Alexis , Du, Mei R. M. , Anderson, Mary Ann , Thijssen, Rachel , Wang, Changqing , Clark, Michael B. , Schuster, Jakob , Collar-Fernández, Coralina , Flensburg, Christoffer , Ryall, James G. , Kariyawasam, Hasaru , Ritchie, Matthew E. , Prawer, Yair David Joseph , Anttila, Casey J. A. , Dong, Xueyi , Huang, David C. S. , Chung, Jin D. , Voogd, Oliver , Naim, Timur , Jabbari, Jafar S. , Gouil, Quentin

in Alternative Splicing / Animal Genetics and Genomics / Animals / biogenesis / Bioinformatics / Biomedical and Life Sciences / chromium / Computer applications / Data analysis / Datasets / Drug resistance / Evolution / Evolutionary Biology / Exons / Gene Expression Profiling - methods / Genes / genome / High-Throughput Nucleotide Sequencing / Human Genetics / Humans / Isoforms / Life Sciences / Long Read Sequencing / Method / Mice / Microbial Genetics and Genomics / Mutation / Nanopore Sequencing - methods / nanopores / Plant Genetics and Genomics / Protein Isoforms - genetics / Protein Isoforms - metabolism / protein synthesis / Protocol / ribosomes / RNA Splicing / RNA, Messenger / Single-cell gene expression / Single-cell multi-omics / species / Splicing / Stem cells / Transcription / Transcriptome / Transcriptomes

2021

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Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

2021

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Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

2021

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Journal Article

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Peng, Hongke,

Amarasinghe, Shanika L.,

Su, Shian,

Ly, Chi Hai,

Majewski, Ian,

Tian, Luyi,

Law, Charity W.,

Roberts, Andrew W.,

Lynch, Gordon S.,

Chan, Audrey,

Lucattini, Alexis,

Du, Mei R. M.,

Anderson, Mary Ann,

Thijssen, Rachel,

Wang, Changqing,

Clark, Michael B.,

Schuster, Jakob,

Collar-Fernández, Coralina,

Flensburg, Christoffer,

Ryall, James G.,

Kariyawasam, Hasaru,

Ritchie, Matthew E.,

Prawer, Yair David Joseph,

Anttila, Casey J. A.,

Dong, Xueyi,

Huang, David C. S.,

Chung, Jin D.,

Voogd, Oliver,

Naim, Timur,

Jabbari, Jafar S.,

Gouil, Quentin

2021

Overview

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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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Alternative Splicing

/ Animal Genetics and Genomics

/ Animals

/ biogenesis

/ Bioinformatics

/ Biomedical and Life Sciences

/ chromium