Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deep sequencing of small and uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

ABSTRACT: Deep sequencing of small and uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

PROVIDER: PRJNA169642 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR517913.fastq.gz	Fastqsanger.gz
	SRR517914.fastq.gz	Fastqsanger.gz
	SRR517915.fastq.gz	Fastqsanger.gz
	SRR517916.fastq.gz	Fastqsanger.gz
	SRR517917.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Deep sequencing of uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

Project description:Our previous experiment on biogenesis mechanisim of stress-inducible antisense RNAs showed that accumulation of antisense RNA in a drought-inducible gene, RD29A locus was decreased in rdr1/2/6 triple mutant. The RD29A antisense RNA did not have CAP structure and poly(A) tail. We applied deep sequencing of uncapped RNA using SOLiD to identify RDR1/2/6-mediated antisense RNAs in genome-wide. We identified 1) 975 RDR1/2/6-mediated antisense RNA loci on which no. of sequence tags is decreased in rdr1/2/6 and makes peak and 2) 1,613 RDR1/2/6-mediated antisense RNA loci on which no. of the tags is decreased in rdr1/2/6 and enriched on antisense strand of exons. They were grouped into 1,959 non-redundant loci.

2017-07-13 | GSE39033 | GEO

Deep sequencing of small RNAs

Project description:Recently, we demonstrated that RDRs had a general function to synthesize antisense RNAs from sense transcripts of protein-coding genes. In this study, we analyzed whether RDR-mediated antisense RNAs were processed into small RNAs by deep sequencing using SOLiD. Deep sequencing identified 1,645 RDR1/2/6-mediated smRNA loci in drought stress and control conditions.

2017-07-13 | GSE39024 | GEO

Evolutionary dynamics of small RNA regulation through genomic hybridization in sugarcane

Project description:The small RNAs and their targets were characterized in sugarcane wild species and cultivars. This was done by deep sequencing the small RNA populations and uncapped mRNAs of young leaves from mature plants.

2023-04-01 | GSE116171 | GEO

Arabidopsis thaliana

Project description:Deep sequencing of uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

| PRJNA169644 | ENA

Large scale sequencing of small RNAs in tomato plants

Project description:In order to compare the small RNA (sRNA) population between the control and Potato spindle tuber viroid (PSTVd) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were mock inoculated. At 21 dpi,tTotal RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

2017-09-20 | GSE70256 | GEO

Indentification samll RNA loci that are synthesized by RNA-dependent RNA polymerases1/2/6

Project description:To identify RDR1/2/6 dependent small RNA loci of transcribed regions under 2hr drought stress- and untreated conditions, expression profiles of small RNA between rdr1/2/6 and wild-type using hi-seq 2000. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2weeks. Then, their plants were transfered to dry plastic dish for 2 hours. small RNA fraction was s extracted from the sample using Ambion mirVana miRNA Isolation Kit. small RNA labrary was constructed using TruSeq Small RNA Library Preparation Kits and applied to hi-seq 2000.

2016-03-31 | E-GEOD-72982 | biostudies-arrayexpress

Deep sequencing of small RNAs in the trasngenic wild type plant and the IWR1-type transcription factor mutant, dms4

Project description:Full title: Deep sequencing of small RNAs in the trasngenic wild type plant (contains trigger and silencer transgenes) and the IWR1-type transcription factor mutant, dms4 RNA-directed DNA methylation (RdDM) in plants requires two RNA polymerase II (PolII)-related RNA polymerases named PolIV and PolV. A genetic screen designed to reveal factors important for RdDM in a developmental context in Arabidopsis identified DEFECTIVE IN MERISTEM SILENCING 4 (DMS4). Unlike other mutants defective in RdDM, dms4 mutants have a pleiotropic developmental phenotype.DMS4 is similar to yeast IWR1, a conserved putative transcription factor that interacts with PolII subunits. In the transgenic system studied, mutations in DMS4 directly or indirectly affect PolIV-dependent secondary siRNAs, PolV-mediated RdDM, PolV-dependent synthesis of intergenic noncoding RNA, and expression of many PolII-driven genes. These data suggest that DMS4 may be a regulatory factor for multiple RNA polymerases, thus explaining its diverse roles in the plant.

2010-03-31 | GSE18302 | GEO

Identification of small RNA loci that are synthesized by RNA-dependent RNA polymerases1/2/6

2016-03-31 | GSE72982 | GEO

GMUCT sequencing of 4 week old leaves in Arabidopsis ABI3:MTA plants

Project description:In order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts

2018-11-09 | GSE108766 | GEO

Small RNAs deep sequencing from sweet potato in wounding stress

Project description:Plant microRNAs (miRNAs) have emerged as important regulators in developmental processes and stress responses in plants. To identify the wound-responsive miRNAs in the leaves of sweet potato, small RNA deep sequencing was conducted on unwounded and wounded leaves (30 min). Total RNAs were isolated for library construction and analyzed by RNA-sequencing via Illumina Genome Analyzer IIx platform. About 16 million total reads were obtained for each sample.

2019-01-15 | GSE115176 | 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