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SRNA sequencing of TRV-infected Nicotiana benthamiana 16c at 29oC

ABSTRACT: sRNA sequencing of TRV-infected Nicotiana benthamiana 16c at 29oC

PROVIDER: PRJEB39525 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4368700.fastq.gz	Fastqsanger.gz
	ERR4368701.fastq.gz	Fastqsanger.gz
	ERR4368702.fastq.gz	Fastqsanger.gz
	ERR4368703.fastq.gz	Fastqsanger.gz
	ERR4368704.fastq.gz	Fastqsanger.gz

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sRNA sequencing of TRV-infected Nicotiana benthamiana 16c

Project description:To systematically investigate viral sRNA production and sRNA-target interaction, we sequenced sRNAs from Tobacco Rattle Virus (TRV)-infected Nicotiana benthamiana at an early (1 week post infection) and late time point (3 weeks post infection). The N. benthamiana 16c plants were infected with TGS-inducing viruses (TRV-35S and TRV-35-2M) and PTGS-inducing viruses (TRV-GFP and TRV-GFP-2M), respectively. TRV-35S is a recombinant TRV containing a 120 nt segment of the 35S promoter. Its derivative, TRV-35S-2M, carrying single nucleotide substitutions (SNS) at every 10 nt within the 120 nt 35S target segment. Same strategy was used to create recombinant TRV-GFP and TRV-GFP-2M targeting GFP coding sequence. According to SNS content, sRNAs from TRV-35S-2M/TRV-GFP-2M infected plants can be separated to yield primary (containing SNSs) and secondary sRNAs (lacking SNSs). Wild Type TRV was used along as viral infection control. Libraries were indexed during PCR amplification (16 cycles) according to the Illumina protocol. See individual sample information for specific index primers used.

2021-01-06 | E-MTAB-8342 | biostudies-arrayexpress

sRNA sequencing of TRV-infected Nicotiana benthamiana 16c at 29oC

Project description:To investigate how high temperature affects sRNA production during virus induced gene silencing (VIGS), we sequenced sRNAs from Tobacco Rattle Virus (TRV)-infected Nicotiana benthamiana kept at 29°C at an early (1 week post infection) and a late time point (3 weeks post infection). To compare sRNA production between virus induced transcriptional gene silencing (ViTGS) and virus induced post-translational gene silencing (ViPTGS) at 29°C, the N. benthamiana 16c plants were infected with TGS-inducing viruses (TRV-35S and TRV-35-2M) and PTGS-inducing viruses (TRV-GFP and TRV-GFP-2M). TRV-35S is a recombinant TRV containing a 120 nt segment of the 35S promoter. Its derivative, TRV-35S-2M, carrying single nucleotide substitutions (SNS) at every 10 nt within the 120 nt 35S target segment. Same strategy was used to create recombinant TRV-GFP and TRV-GFP-2M targeting GFP coding sequence. According to SNS content, sRNAs from TRV-35S-2M/TRV-GFP-2M infected plants can be separated to yield primary (containing SNSs) and secondary sRNAs (lacking SNSs). Wild Type TRV was used along as viral infection control. Libraries were indexed during PCR amplification (16 cycles) according to the Illumina protocol. See individual sample information for specific index primers used.

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sRNA sequencing of TRV-infected Nicotiana benthamiana 16c

Project description:sRNA sequencing of TRV-infected Nicotiana benthamiana 16c

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NGS data of Nicotiana benthamiana 16c plants after CRISPR/Cas9 gene editing

Project description:Provided data came from a detailed study on Nicotiana benthamiana 16c plants where we use Tobacco Rattle Virus (TRV) as a molecular switch to change the chromatin state of a reporter gene (P35S::GFP) from an actively transcribed to a transcriptionally silenced state. Our approach enables us to interrogate different chromatin states of the same locus with the same set of CRISPR/Cas9 genome editing reagents and systematically describe the effect of chromatin state on the frequency and type of mutations induced at various Cas9 targets in a huge set of independently edited cells.

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Project description:We report the sRNA profile upon dsRNA spraying on 16C (Nicotiana benthamiana) plants. In this experiment we could detect only the degradation products of the dsRNA, which indicates absence of further processing of the dsRNA by RNAi machinery

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NGS data of Nicotiana benthamiana 16c plants after CRISPR/Cas9 gene editing

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