Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SRNA sequencing of TRV-infected Nicotiana benthamiana 16c

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

PROVIDER: PRJEB34459 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3525330.fastq.gz	Fastqsanger.gz
	ERR3525321.fastq.gz	Fastqsanger.gz
	ERR3525322.fastq.gz	Fastqsanger.gz
	ERR3525323.fastq.gz	Fastqsanger.gz
	ERR3525324.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

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.

2021-06-28 | E-MTAB-9394 | biostudies-arrayexpress

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

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

| PRJEB39525 | ENA

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.

2022-05-04 | E-MTAB-10256 | biostudies-arrayexpress

Nicotiana benthamiana

Project description:Nicotiana benthamiana

| PRJNA256274 | ENA

Nicotiana benthamiana

Project description:sRNA sequences of Nicotiana benthamiana responding to Alternaria longipes infection

| PRJNA708140 | ENA

High-pressure-sprayed double stranded RNA does not induce RNA interference of a reporter gene

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

2020-12-01 | GSE160110 | GEO

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

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

| PRJEB43846 | ENA

Small RNAs from Nicotiana benthamiana leaves

Project description:Small RNA expression from Nicotiana benthamiana leaves was profiled with the primary goal of ascertaining microRNA isoform diversity for known, conserved families. A secondary goal was to provide a baseline small RNA expression atlas for this species and tissue.

2014-02-10 | GSE48886 | GEO

RNA sequencing of NlCSP11-infiltrated Nicotiana benthamiana

Project description:In order to find the differentially expressed RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11, 35S-XopQ and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed RNAs in the infiltrated leaves (NlCSP11_Z/XopQ_Z) and the upper uninfiltrated leaves (NlCSP11_U/XopQ_U) of N. benthamiana. KEGG annotation revealed a large number of differentially expressed RNAs involved in plant-pathogen interactions, indicating that NlCSP11 resulted in a more strong systemic resistance in N. benthamiana.

2024-05-30 | GSE267686 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data