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Bacterial & Archaeal Transcriptome Meta-analysis Project.

Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

This is a collection of RNA-seq datasets spanning Archaea and Bacteria. Each dataset has been converted into a consistent format, plotfiles, containing read-depths for each position of the corresponding genome. These files can be read by genome viewing tools such as Artemis so RNA-seq data can be viewed in the context of genome annotations.

Datasets for the next release:

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling.
Li S, Dong X, Su Z.
BMC Genomics. 2013 Jul 30;14(1):520.
http://www.biomedcentral.com/1471-2164/14/520/abstract

Computational analysis of bacterial RNA-Seq data.
McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B.
Nucleic Acids Res. 2013 May 28
http://nar.oxfordjournals.org/content/early/2013/05/28/nar.gkt444.long

RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
Toffano-Nioche C, Ott A, Crozat E, Nguyen AN, Zytnicki M, Leclerc F, Forterre P, Bouloc P, Gautheret D.
RNA Biol. 2013 Jul 2;10(7).

Determination of sRNA Expressions by RNA-seq in Yersinia pestis Grown In Vitro and during Infection
Yan et al. 
PLoS One. 2013; 8(9): e74495.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770706/

RNA-Seq Analysis of Mycobacterium avium Non-Coding Transcriptome
Ignatov et al. 
PLoS One. 2013; 8(9): e74209. 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0074209

Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria
Moody et al. 
BMC Genomics. 2013
http://www.biomedcentral.com/1471-2164/14/558/abstract

Revealing of Mycobacterium marinum Transcriptome by RNA-seq
Wang et al.
PLoS ONE

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed
within a productive fermentation
Wiegand et al.
BMC Genomics 2013, 14:667

Probing bacterial metabolism during infection using high-resolution transcriptomics
Jorth et al.
Aggregatibacter actinomycetemcomitans
http://jb.asm.org/content/early/2013/08/19/JB.00875-13.short?rss=1

Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
Pfeifer-Sancar et al.
http://www.biomedcentral.com/1471-2164/14/888/abstract

Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2
Dam et al.
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12367/abstract

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A RNA Encyclopaedia for Bacteria and Archaea

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