Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

ABSTRACT: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

PROVIDER: PRJNA477783 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7419811_1.fastq.gz	Fastqsanger.gz
	SRR7419811_2.fastq.gz	Fastqsanger.gz
	SRR7419812_1.fastq.gz	Fastqsanger.gz
	SRR7419812_2.fastq.gz	Fastqsanger.gz
	SRR7419813_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

| PRJNA480216 | ENA

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

| PRJNA477980 | ENA

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

Project description:Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and trascriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

2021-06-24 | GSE116774 | GEO

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

2021-06-24 | GSE116214 | GEO

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

Project description:An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

| PRJNA476254 | ENA

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

Project description:Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and transcriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

2021-06-24 | GSE115843 | GEO

Sequencing of rice degradome

Project description:miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs. Two rice samples, 3-week-old seedling and young panicles were included in the study.

2009-11-23 | E-GEOD-18248 | biostudies-arrayexpress

A degradome sequencing of rice mesocotyl from darkness to light exposure

Project description:Light exposure quickly inhibits the elongation of mesocotyl of rice seedling. The two corresponding periods from darkness to loght (D_5d, L_1h) were selected to perform degradome sequencing.

2021-08-21 | GSE136140 | GEO

An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-24 | GSE116275 | GEO

Unique transcriptome and gene expression analysis of rice seedling reveals different cadmium response regulatory mechanisms between Indica and Japonica rice

Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.

2023-01-02 | GSE196229 | 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