Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

(2020) Alina Glaub et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

(2020) Diego Rivera Gelsinger et al.   NUCLEIC ACIDS RESEARCH

Nuclease-mediated depletion biases in ribosome footprint profiling libraries

(2020) Boris Zinshteyn et al.   RNA

The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom

(2019) Katharina Schwarze et al.   GENETICS IN MEDICINE

Efficient depletion of ribosomal RNA for RNA sequencing in planarians

(2019) Iana V. Kim et al.   BMC GENOMICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

(2018) Sarah M. Hücker et al.   BMC EVOLUTIONARY BIOLOGY

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

(2018) Zachary T. Herbert et al.   BMC GENOMICS

Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature

(2018) Katharina Schwarze et al.   GENETICS IN MEDICINE

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

(2017) Olga E. Petrova et al.   Scientific Reports

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis

(2015) Betty Y. Chung et al.   RNA

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

(2014) Richard Landstorfer et al.   BMC GENOMICS

Streptavidin–biotin technology: improvements and innovations in chemical and biological applications

(2013) Christopher M. Dundas et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

After the gold rush

(2013) Neil Hall   GENOME BIOLOGY

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR

(2011) Kang Zhou et al.   BMC MOLECULAR BIOLOGY

Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures

(2011) Konstantinos Minas et al.   FEMS MICROBIOLOGY LETTERS

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes

(2010) Dawn Ciulla et al.   GENOME BIOLOGY

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

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