Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nicotiana benthamiana

ABSTRACT: Transient expression of intron-containing transgenes generates non-spliced aberrant pre-mRNAs that are processed into siRNAs

PROVIDER: PRJNA481240 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7535030.fastq.gz	Fastqsanger.gz
	SRR7535031.fastq.gz	Fastqsanger.gz
	SRR7535032.fastq.gz	Fastqsanger.gz
	SRR7535033.fastq.gz	Fastqsanger.gz
	SRR7535034.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Nicotiana benthamiana

Project description:sRNA sequencing to study assorted processing of synthetic trans-acting siRNAs and its activity in antiviral resistance

| PRJNA285263 | ENA

Nicotiana Benthamiana

Project description:pssRNAit: a web server for designing highly effective and specific plant RNAi siRNAs with genome-wide off-target gene assessment

| PRJNA525845 | ENA

Identification of NMD regulated genes in Nicotiana benthamiana

Project description:Nonsense mediated decay (NMD) is a translation termination coupled quality control system. NMD identifies and degrades aberrant mRNAs containing premature termination codons, thereby preventing the accumulation of detrimental truncated proteins. NMD also controls the expression of several normal mRNAs and non-coding transcripts. RNA-seq assays were conducted to identify the NMD regulated genes in Arabidopsis. However, NMD targets have not been studied in other plants. To identify the conserved NMD targets, we wanted to identify the NMD regulated genes in Nicotiana benthamiana model species. Virus induced gene silencing was used to inactivate UPF1 NMD key factor in N. benthamiana, and then comparative RNA-seq experiment was carried out using UPF1-silenced and control–silenced plants. We found that in N. benthamiana significantly more genes are controlled by NMD than in Arabidopsis and that, surprisingly few conserved NMD targets can be recognized. These results suggest that while the mechanism of NMD is highly conserved, the set of NMD controlled genes can be quickly changed in plants.

2019-07-01 | GSE109130 | GEO

Profile of small interfering RNAs derived from Beet black scorch virus and its associated satellite RNA in Nicotiana benthamiana

Project description:Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. Here we find that the sat-RNA of Beet black scorch virus (BBSV) enhances both the accumulation and the systemic infection of its helper virus in the Nicotiana benthamiana (N. benthamiana). Besides, the infection of BBSV is higher efficient in low temperature (18ºC) than room temperature (25ºC), suggesting that BBSV is temperature sensitive. To explore the effect of temperature and sat-RNA on the silencing induced by BBSV, we cloned and sequenced the total small RNAs produced during infection of BBSV alone or with its sat-RNA under different temperature. Our results shows that the size profile of the siRNAs derived from either BBSV or coinfection with sat-RNA are 22 nucleotide (nt), followed by 21-nt reads and other length reads. Notably, more than 80% of the total small RNAs sequenced from plants infected with BBSV alone were BBSV-siRNAs, whereas the abundance of sat-RNA-derived siRNAs were higher than BBSV-siRNAs in the co-infected plants, indicating sat-RNA involved in gene silencing as a surrogacy of BBSV. Interestingly, the 5′ termini of siRNAs derived from BBSV and sat-RNA were dominated by Uridines (U) and Adenines (A), respectively. Consistently, the infection of BBSV alone or with sat-RNA induces high accumulation of Argonaute 1 (AGO1) and AGO2, respectively. Our work reveals the profiles of siRNAs of BBSV and sat-RNA and provides a new clue to investigate the complicated interaction between the helper virus and sat-RNA.

2017-02-09 | GSE80694 | GEO

Small RNA profile in fully grown mammalian oocytes

Project description:We aim to comprehensively characterize the small RNA population in oocytes Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals. Keywords: small RNAs profile

2008-03-28 | GSE10364 | GEO

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

Nicotiana benthamiana

Project description:RNA-Seq analysis of mycorrhizal and non-mycorrhizal roots of Nicotiana benthamiana

| PRJDB3374 | ENA

Nicotiana benthamiana

Project description:Nicotiana benthamiana Raw sequence reads

| PRJNA355339 | ENA

Nicotiana benthamiana

Project description:Nicotiana benthamiana Transcriptome or Gene expression

| PRJNA288746 | ENA

Nicotiana benthamiana

Project description:Profile of small interfering RNAs derived from Beet black scorch virus and its associated satellite RNA in Nicotiana benthamiana

| PRJNA319720 | ENA

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