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ABSTRACT: Diretmus argenteus (silver spinyfin) genome, fDirArg3, sequence data

PROVIDER: PRJNA1237423 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR32745957_subreads.fastq.gz	Fastqsanger.gz
	SRR32745958_subreads.fastq.gz	Fastqsanger.gz
	SRR32745959_subreads.fastq.gz	Fastqsanger.gz
	SRR32745960_subreads.fastq.gz	Fastqsanger.gz
	SRR32745961_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to chronic exposure to silver nitrate at 4 μg/mL concentration. Methods: mRNA was extracted from non-treated and silver nitrate-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were paired-end sequenced (100-nt read length) on an Illumina Nova Seq6000 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 20.0.4, Qiagen). Results: Chronic exposure of A. thaliana plants to silver nitrate caused a change in the abundance of transcripts: AT2G01520 and AT4G12550, but no measureable impact on the rest of the transcriptome. Conclusions: Exposure of A. thaliana to silver nitrate at 4 μg/mL has minor impact on the transcriptome.

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Project description:Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to sublethal concentrations of silver nanoparticles in order to gain insight into phytotoxicity caused by these nanomaterials. Methods: mRNA was extracted from non-treated and silver nanoparticle-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were single-end sequenced (100-nt read length) on an Illumina HiSeq2500 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 7.0.40, Qiagen). Results: Chronic exposure of A. thaliana plants to silver nanoparticles caused a change in abundance of transcripts involved in cell wall synhtesis and response to oxidative and biotic stress-related genes. Conclusions: While exposure to silver nanoparticle lead to gene expression changes, the reduction in chlorophyll concentration and carbon assimilation rate measured in exposed plants cannot be attributed to a shift in photosynthesis-related gene regulation.

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