Mapping and quantifying mammalian transcriptomes by RNA-Seq

A Mortazavi, BA Williams, K McCue, L Schaeffer… - Nature …, 2008 - nature.com
We have mapped and quantified mouse transcriptomes by deeply sequencing them and
recording how frequently each gene is represented in the sequence sample (RNA-Seq) …

Universal alternative splicing of noncoding exons

IW Deveson, ME Brunck, J Blackburn, E Tseng, T Hon… - Cell Systems, 2018 - cell.com
The human transcriptome is so large, diverse, and dynamic that, even after a decade of
investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions …

Spliced synthetic genes as internal controls in RNA sequencing experiments

SA Hardwick, WY Chen, T Wong, IW Deveson… - Nature …, 2016 - nature.com
RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed
genes and provide a global profile of the transcriptome. However, the size and diversity of …

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

M Sultan, MH Schulz, H Richard, A Magen… - Science, 2008 - science.org
The functional complexity of the human transcriptome is not yet fully elucidated. We report a
high-throughput sequence of the human transcriptome from a human embryonic kidney and …

Direct RNA sequencing

F Ozsolak, AR Platt, DR Jones, JG Reifenberger… - Nature, 2009 - nature.com
Our understanding of human biology and disease is ultimately dependent on a complete
understanding of the genome and its functions. The recent application of microarray and …

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

MB Clark, TR Mercer, G Bussotti, T Leonardi… - Nature …, 2015 - nature.com
We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing
(CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and …

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

C Trapnell, BA Williams, G Pertea, A Mortazavi… - Nature …, 2010 - nature.com
High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery
and abundance estimation,,. However, this would require algorithms that are not restricted …

IVT-seq reveals extreme bias in RNA sequencing

NF Lahens, IH Kavakli, R Zhang, K Hayer, MB Black… - Genome biology, 2014 - Springer
Background RNA-seq is a powerful technique for identifying and quantifying transcription
and splicing events, both known and novel. However, given its recent development and the …

A single-molecule long-read survey of the human transcriptome

D Sharon, H Tilgner, F Grubert, M Snyder - Nature biotechnology, 2013 - nature.com
Global RNA studies have become central to understanding biological processes, but
methods such as microarrays and short-read sequencing are unable to describe an entire …

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing

GK Marinov, BA Williams, K McCue… - Genome …, 2014 - genome.cshlp.org
Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering
cell-to-cell variation in gene expression, transcript processing and editing, and regulatory …