RNA-Seq methods for transcriptome analysis

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes

(2015) Fredrik Mertens et al.   GENES CHROMOSOMES & CANCER

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing

(2015) Eric Samorodnitsky et al.   HUMAN MUTATION

Employment of digital gene expression profiling to identify potential pathogenic and therapeutic targets of fulminant hepatic failure

(2015) En-Qiang Chen et al.   Journal of Translational Medicine

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

(2015) Michael B Clark et al.   NATURE METHODS

TARDIS, a targeted RNA directional sequencing method for rare RNA discovery

(2015) Maximiliano M Portal et al.   Nature Protocols

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues ofSalvia miltiorrhizaand tanshinone biosynthesis

(2015) Zhichao Xu et al.   PLANT JOURNAL

PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome

(2015) P. F. Harrison et al.   RNA

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Single-Cell Analysis in Cancer Genomics

(2015) Assieh Saadatpour et al.   TRENDS IN GENETICS

Splicing noncoding RNAs from the inside out

(2015) Li Yang   Wiley Interdisciplinary Reviews-RNA

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

(2015) Brad T. Townsley et al.   Frontiers in Plant Science

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Single Cell Transcriptome Amplification with MALBAC

(2015) Alec R. Chapman et al.   PLoS One

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

(2015) Jonathan A. Scolnick et al.   PLoS One

Digital Encoding of Cellular mRNAs Enabling Precise and Absolute Gene Expression Measurement by Single-Molecule Counting

(2014) Glenn K. Fu et al.   ANALYTICAL CHEMISTRY

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage

(2014) Stuart K Archer et al.   BMC GENOMICS

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing

(2014) Evgeny A. Moskalev et al.   LUNG CANCER

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments

(2014) Erin E. Heyer et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

(2014) Glenn K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Seeing is believing: new methods for in situ single-cell transcriptomics

(2014) Gal Avital et al.   GENOME BIOLOGY

Next Generation Sequencing Reveals Skewing of the T and B Cell Receptor Repertoires in Patients with Wiskott–Aldrich Syndrome

(2014) Amy E. O’Connell et al.   Frontiers in Immunology

Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS)

(2014) Hua Fang et al.   OncoImmunology

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads

(2013) Jikun Wu et al.   BIOINFORMATICS

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq

(2013) Chenglin Liu et al.   BMC BIOINFORMATICS

A new method for stranded whole transcriptome RNA-seq

(2013) David F.B. Miller et al.   METHODS

Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq

(2013) Sabarinath Jayaseelan et al.   METHODS

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

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

(2013) Xian Adiconis et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

(2013) Zhifu Sun et al.   PLoS One

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peregrine

(2013) Stanley A. Langevin et al.   RNA Biology

Alternative cleavage and polyadenylation: the long and short of it

(2013) Bin Tian et al.   TRENDS IN BIOCHEMICAL SCIENCES

Quantitative Transcriptomics using Designed Primer-based Amplification

(2013) Vipul Bhargava et al.   Scientific Reports

Ribonuclease III mechanisms of double-stranded RNA cleavage

(2013) Allen W. Nicholson   Wiley Interdisciplinary Reviews-RNA

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

(2013) Matteo Carrara et al.   Biomed Research International

Preparing Unbiased T-Cell Receptor and Antibody cDNA Libraries for the Deep Next Generation Sequencing Profiling

(2013) Ilgar Z. Mamedov et al.   Frontiers in Immunology

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A bias-reducing strategy in profiling small RNAs using Solexa

(2011) G. Sun et al.   RNA

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Multi-targeted priming for genome-wide gene expression assays

(2010) Aleksandra B Adomas et al.   BMC GENOMICS

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

Next-generation tag sequencing for cancer gene expression profiling

(2009) A. S. Morrissy et al.   GENOME RESEARCH

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

(2009) Joshua Z Levin et al.   GENOME BIOLOGY

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing

(2007) Markus Hafner et al.   METHODS