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OdHalCaeu

ABSTRACT: Halisarca caerulea, genomic and transcriptomic data

PROVIDER: PRJEB62892 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR11547911_1.fastq.gz	Fastqsanger.gz
	ERR11547911_2.fastq.gz	Fastqsanger.gz
	ERR11547912_1.fastq.gz	Fastqsanger.gz
	ERR11547912_2.fastq.gz	Fastqsanger.gz
	ERR11547913_1.fastq.gz	Fastqsanger.gz

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odHalCaeu

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Identification of early response genes to Pratylenchus coffeae in resistant ramie by digital gene expression analysis (leaves)

Project description:Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between CK and Cocytodes caerulea Guenée challenged (CH) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation. Leaf samples of Cocytodes caerulea infested (T2) and un-infested (T1) ramie were RNA-Seq sequenced to compare differented expressed genes.

2015-03-04 | E-GEOD-66447 | biostudies-arrayexpress

Halisarca dujardinii

Project description:Halisarca dujardinii overview

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Genome-wide expression analysis of ramie [Boehmeria nivea (L.) Gaudich] genes in response to ramie moth [Cocytodes coerulea Guenée] infestation

Project description:Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between Cocytodes caerulea Guenée challenged (CH) and unchallenged (CK) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation.

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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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