RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

JC Marioni, CE Mason, SM Mane, M Stephens… - Genome …, 2008 - genome.cshlp.org
Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for
genotyping, analysis of methylation patterns, and identification of transcription factor binding …

RNA-Seq and its applications: a new technology for transcriptomics

YX Qi, YB Liu, WH Rong - Yi Chuan= Hereditas, 2011 - europepmc.org
The transcriptome is the complete set of transcripts for certain type of cells or tissues in a
specific developmental stage or physiological condition. Transcriptome analysis can provide …

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

M Lohse, AM Bolger, A Nagel, AR Fernie… - Nucleic acids …, 2012 - academic.oup.com
Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide
researchers with unprecedentedly large data sets and open new perspectives in …

RNA-seq differential expression studies: more sequence or more replication?

Y Liu, J Zhou, KP White - Bioinformatics, 2014 - academic.oup.com
Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression
studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low …

Introduction to single‐cell RNA sequencing

TK Olsen, N Baryawno - Current protocols in molecular biology, 2018 - Wiley Online Library
During the last decade, high‐throughput sequencing methods have revolutionized the entire
field of biology. The opportunity to study entire transcriptomes in great detail using RNA …

Differential expression in RNA-seq: a matter of depth

S Tarazona, F García-Alcalde, J Dopazo… - Genome …, 2011 - genome.cshlp.org
Next-generation sequencing (NGS) technologies are revolutionizing genome research, and
in particular, their application to transcriptomics (RNA-seq) is increasingly being used for …

Comparative analysis of RNA sequencing methods for degraded or low-input samples

X Adiconis, D Borges-Rivera, R Satija, DS DeLuca… - Nature …, 2013 - nature.com
RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply
to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers …

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

CR Williams, A Baccarella, JZ Parrish, CC Kim - BMC bioinformatics, 2017 - Springer
Background RNA-Seq has supplanted microarrays as the preferred method of transcriptome-
wide identification of differentially expressed genes. However, RNA-Seq analysis is still …

[HTML][HTML] The START App: a web-based RNAseq analysis and visualization resource

JW Nelson, J Sklenar, AP Barnes, J Minnier - Bioinformatics, 2017 - academic.oup.com
Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful
methodology to quantify global gene expression patterns in various contexts from single …

Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly (A) selection

Z Zhang, WE Theurkauf, Z Weng, PD Zamore - Silence, 2012 - Springer
Background High throughput DNA sequencing technology has enabled quantification of all
the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq) …