Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Lott, Steffen C.; Wolfien, Markus; Riege, Konstantin; Bagnacani, Andrea; Hoffmann, Steve; Hess, Wolfgang R.

doi:10.1016/j.jbiotec.2017.06.1203

Cited by 11 publications

(8 citation statements)

References 155 publications

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“…A recent study applied GLASSgo to exhaustively detect homologs of the sRNA OxyS ( 24 ). Another detailed use case is given in ( 25 ), where GLASSgo plays a key role in the de novo discovery of sRNAs.…”

Section: Methods and Servicesmentioning

confidence: 99%

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Raden

Ali

Alkhnbashi

et al. 2018

Nucleic Acids Research

130

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The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.

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Section: Methods and Servicesmentioning

confidence: 99%

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Raden

Ali

Alkhnbashi

et al. 2018

Nucleic Acids Research

130

View full text Add to dashboard Cite

show abstract

“…1 Workflow for the identification of sRNA candidates through mdRNA-Seq analysis of Prochlorococcus-related cDNA sequences from environmental samples. The workflow was modified from previous publications [32,54] and follows the recommendations given in the reference [55].…”

Section: Validation and Characterization Of Predicted Srnas And Asrnamentioning

confidence: 99%

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

et al. 2020

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Small regulatory RNAs and antisense RNAs play important roles in the regulation of gene expression in bacteria but are underexplored, especially in natural populations. While environmentally relevant microbes often are not amenable to genetic manipulation or cannot be cultivated in the laboratory, extensive metagenomic and metatranscriptomic datasets for these organisms might be available. Hence, dedicated workflows for specific analyses are needed to fully benefit from this information. Here, we identified abundant sRNAs from oceanic environmental populations of the ecologically important primary producer Prochlorococcus starting from a metatranscriptomic differential RNA-Seq (mdRNA-Seq) dataset. We tracked their homologs in laboratory isolates, and we provide a framework for their further detailed characterization. Several of the experimentally validated sRNAs responded to ecologically relevant changes in cultivation conditions. The expression of the here newly discovered sRNA Yfr28 was highly stimulated in low-nitrogen conditions. Its predicted top targets include mRNAs encoding cell division proteins, a sigma factor, and several enzymes and transporters, suggesting a pivotal role of Yfr28 in the coordination of primary metabolism and cell division. A cis-encoded antisense RNA was identified as a possible positive regulator of atpF encoding subunit b' of the ATP synthase complex. The presented workflow will also be useful for other environmentally relevant microorganisms for which experimental validation abilities are frequently limiting although there is wealth of sequence information available.

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“…The RBC-Freiburg focuses on the analysis of RNA-RNA and RNA-protein interactions 39 , RBC-Leipzig on the analysis of non-coding RNAs and RNA structure 40 and RBC-Berlin on RNA-binding proteins and post-transcriptional regulation 41 . The partner project de.STAIR consists of three sites: de.STAIR-Freiburg working on the regulatory RNA interaction and integration, de.STAIR-Jena on the causes and effects of quantitative and qualitative expression changes and de.STAIR-Rostock on RNA-Seq workflow specification and technical integration 42 . The second partner project de.NBI-epi is located in Berlin and in Freiburg and is focusing on Computational Epigenetics.…”

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

et al. 2020

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The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.

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Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Cited by 11 publications

References 155 publications

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

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