Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development

(2015) Robert Lowe et al.   BMC GENOMICS

Transcriptome analysis of ageing in uninjured human Achilles tendon

(2015) Mandy Peffers et al.   ARTHRITIS RESEARCH & THERAPY

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

(2015) Brendan P. Hodkinson et al.   Advances in Wound Care

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

(2014) Ghanasyam Rallapalli et al.   BMC GENOMICS

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis

(2014) F. Finotello et al.   Briefings in Functional Genomics

Detecting and characterizing circular RNAs

(2014) William R Jeck et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP

(2014) Vahid Khoddami et al.   Nature Protocols

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A multispecies polyadenylation site model

(2013) Eric S Ho et al.   BMC BIOINFORMATICS

High throughput characterizations of poly(A) site choice in plants

(2013) Liuyin Ma et al.   METHODS

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

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

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

(2013) Zhihua Jiang et al.   PLoS One

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation

(2013) Juan Mata   RNA Biology

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

(2013) M. Schlackow et al.   RNA

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

(2013) Teresa Cortes et al.   Cell Reports

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Old can be new again: HAPPY whole genome sequencing, mapping and assembly

(2012) Zhihua Jiang et al.   International Journal of Biological Sciences

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

(2012) Mainul Hoque et al.   NATURE METHODS

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

(2012) Julia Salzman et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

E2F mediates enhanced alternative polyadenylation in proliferation

(2012) Ran Elkon et al.   GENOME BIOLOGY

Length bias correction for RNA-seq data in gene set analyses

(2011) Liyan Gao et al.   BIOINFORMATICS

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An experimentally anchored map of transcriptional start sites in the model cyanobacteriumSynechocystissp. PCC6803

(2011) Jan Mitschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) P. J. Shepard et al.   RNA

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

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

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Massive transcriptional start site analysis of human genes in hypoxia cells

(2009) Katsuya Tsuchihara et al.   NUCLEIC ACIDS RESEARCH

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

(2009) Zhe Ji et al.   PLoS One

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Poly A- Transcripts Expressed in HeLa Cells

(2008) Qingfa Wu et al.   PLoS One

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE