How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression

(2011) Anjali Mandlik et al.   Cell Host & Microbe

Genome-wide detection of novel regulatory RNAs in E. coli

(2011) R. Raghavan et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Genome-Wide Identification of Transcription Start Sites Yields a Novel Thermosensing RNA and New Cyclic AMP Receptor Protein-Regulated Genes in Escherichia coli

(2011) R. Raghavan et al.   JOURNAL OF BACTERIOLOGY

NanoRNAs Prime Transcription Initiation In Vivo

(2011) Seth R. Goldman et al.   MOLECULAR CELL

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems

(2010) K.-S. Kim et al.   JOURNAL OF BACTERIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma 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

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

(2010) Niall J Lennon et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Mining regulatory 5′UTRs from cDNA deep sequencing datasets

(2009) Jonathan Livny et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

(2009) Jane M. Liu et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

(2008) Elizabeth M. Fozo et al.   MOLECULAR MICROBIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

(2008) Jonathan Livny et al.   PLoS One