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OdIrcVari

ABSTRACT: Ircinia variabilis, genomic and transcriptomic data

PROVIDER: PRJEB70430 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR12321252_1.fastq.gz	Fastqsanger.gz
	ERR12321252_2.fastq.gz	Fastqsanger.gz
	ERR12321253_1.fastq.gz	Fastqsanger.gz
	ERR12321253_2.fastq.gz	Fastqsanger.gz
	ERR12321254_1.fastq.gz	Fastqsanger.gz

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Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures. Hybridizations used NimbleGen expression array chips (Product no. A4385-00-01, platform accession no GPL15883) designed against the 5,657 ORFs encoded in the A. variabilis genome (GenBank accession no. CP000117). Each ORF was represented by seventeen 60-mer oligonucleotides. Each oligonucleotide was present in four internal replicates. The twenty-seven microarray data files were normalized against each other. Expression array data were analyzed using ArrayStar 3.0 (DNASTAR, Madison, WI).

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Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

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