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DcSalRamo

ABSTRACT: Salicornia ramosissima, genomic and transcriptomic data

PROVIDER: PRJEB61610 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	ERR11271531_1.fastq.gz	Fastqsanger.gz
	ERR11271531_2.fastq.gz	Fastqsanger.gz
	ERR11279087.fastq.gz	Fastqsanger.gz
	ERR11279088.fastq.gz	Fastqsanger.gz
	ERR12642430_1.fastq.gz	Fastqsanger.gz

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dcSalRamo

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Project description:Transcriptomic profiling of T. chinensis and T. ramosissima shows responses due to water deficit that are common between the two species and differences that shows their invasiveness originating from southern and northern united states. Several drought related genes that were up-regulated common in both species and transcription factors unique to T.chinensis and T. ramosissima were also found. Gene Ontology classification shows similar functional categories in both the species. Differences in two species due to water deficit were also illustrated in networks constructed from genes enriched in biological processes and molecular functions.

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Project description:Tamarix ramosissima

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Project description:This project focused on the identification of membrane proteins involved in salinity tolerance in the halophyte Salicornia bigelovii. Salicornia bigelovii plants were treated with 0, 50, 200, and 600 mM NaCl for 6 weeks. Membrane preparations for each treatment were obtained in triplicates and were separated into 12 fractions per sample through a continuous sucrose gradient. Based on protein relative abundances per fraction, organellar membrane proteomes were generated. Protein abundances were also compared across treatments.

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tfGorAlbo

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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.

2017-12-18 | PXD006238 | Pride

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