Opportunities and challenges in long-read sequencing data analysis

SL Amarasinghe, S Su, X Dong, L Zappia, ME Ritchie… - Genome biology, 2020 - Springer
Long-read technologies are overcoming early limitations in accuracy and throughput,
broadening their application domains in genomics. Dedicated analysis tools that take into …

[HTML][HTML] Identifying cell populations with scRNASeq

TS Andrews, M Hemberg - Molecular aspects of medicine, 2018 - Elsevier
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the
transcriptome of individual cells. However, the data from scRNASeq experiments is often …

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

SA Hardwick, W Hu, A Joglekar, L Fan, PG Collier… - Nature …, 2022 - nature.com
Single-nuclei RNA sequencing characterizes cell types at the gene level. However,
compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack …

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen… - Nature …, 2021 - nature.com
High-throughput amplicon sequencing of large genomic regions remains challenging for
short-read technologies. Here, we report a high-throughput amplicon sequencing approach …

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

I Gupta, PG Collier, B Haase, A Mahfouz… - Nature …, 2018 - nature.com
Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and
sorted cells to characterize transcriptomes,,,,,,,,,,, but applying this technology to single cells …

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

A Byrne, AE Beaudin, HE Olsen, M Jain, C Cole… - Nature …, 2017 - nature.com
Understanding gene regulation and function requires a genome-wide method capable of
capturing both gene expression levels and isoform diversity at the single-cell level. Short …

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

A Lafzi, C Moutinho, S Picelli, H Heyn - Nature protocols, 2018 - nature.com
Single-cell RNA sequencing is at the forefront of high-resolution phenoty** experiments
for complex samples. Although this methodology requires specialized equipment and …

Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

TA Ray, K Cochran, C Kozlowski, J Wang… - Nature …, 2020 - nature.com
Genes encoding cell-surface proteins control nervous system development and are
implicated in neurological disorders. These genes produce alternative mRNA isoforms …

The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome

IW Deveson, SA Hardwick, TR Mercer, JS Mattick - Trends in Genetics, 2017 - cell.com
The combination of pervasive transcription and prolific alternative splicing produces a
mammalian transcriptome of great breadth and diversity. The majority of transcribed …

The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing

C Foord, J Hsu, J Jarroux, W Hu, N Belchikov… - nature methods, 2023 - nature.com
Long-read sequencing has become a widely employed technology that enables a
comprehensive view of RNA transcripts. Here, we discuss the importance of long-read …