Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Akihiro Matsui

PROVIDER: E-GEOD-72982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of small 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.

2016-03-31 | GSE72982 | GEO

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under rehydration

Project description:To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress and 2hr rehydration, expression profiles of Poly (A+) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 weeks. Then, the plants were transferred to plastic dish and kept for 2hr. Poly (A+) RNA from 100Î¼g total RNA by treating with Ambion Poly A purist twice.5 ng of Poly (A+) RNA were used for the expresion profiling using the custom array (GPL19830).

2016-07-31 | E-GEOD-83846 | biostudies-arrayexpress

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress

Project description:To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress, expression profiles of Poly (A+) RNA and Poly (A-) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 hours. Then, the plants were transferred to plastic dish and kept for 1 week. Poly (A+) RNA and Poly (A-) fractions were separated from 100Î¼g total RNA by treating with Ambion Poly A purist twice. Poly (A-) RNA sample was prepared by depleting rRNA using Invitrogen RiboMinus Plant Kit. 5 ng of Poly (A+) RNA and 1.4 Î¼g of Poly (A-) RNA samples were used for the expression profiling using the custom array (GPL19830).

2016-07-31 | E-GEOD-72309 | biostudies-arrayexpress

Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis

Project description:Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis This study constructed and sequenced two independent small RNA libraries from the upper uninoculated leaves of (i) WT Arabidopsis plants 14 d after mock inoculation and of (ii) rdr1 rdr6 plants 14 d after infection with Fny CMV-Δ2b, and one library each from the upper uninoculated leaves of (iii) WT, (iv) rdr1, and (v) rdr6 plants 14 d after infection with TuMV-GFP. Coimmunoprecipitation with FLAG- and HA-specific antibodies was used to obtain (vi,vii) AGO1 and (viii,ix) AGO2 complexes, respectively, from the FLAG-AGO1/ago1-36 and HA-AGO2 plants 14 d after infection with Fny CMV-Δ2b for extracting total loaded small RNAs for the construction and sequencing of small RNA libraries.

2014-08-30 | E-GEOD-60929 | biostudies-arrayexpress

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under rehydration

2016-07-31 | GSE83846 | GEO

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress

2016-07-31 | GSE72309 | GEO

TMV-derived Small RNAs Reveals Role for Arabidopsis thaliana RNA-dependent RNA Polymerases in Viral siRNA Biogenesis

Project description:Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus. The TMV-Cg genome harbored multiple, highly reproducible small RNA-generating hot spots that corresponded to regions with no apparent local hairpin-forming capacity. Significantly, both the rdr1 and rdr6 mutants exhibited globally reduced levels of viral small RNA production as well as reduced strand bias in viral small RNA population, revealing an important role for these host RDRs in viral siRNA biogenesis. In addition, an informatics analysis showed that a large set of host genes could be potentially targeted by TMV-Cg-derived siRNAs for posttranscriptional silencing, raising the interesting possibility for a hidden layer of widespread virus-host interactions that may contribute to viral pathogenicity and host specificity. Profiling of TMV-Cg derived small RNAs in systemically infected tissues of wild type (Col-0) Arabidopsis as well as the rdr1and rdr6 mutants, at 3 days post-infection.

2009-03-24 | E-GEOD-12918 | biostudies-arrayexpress

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress

A user-friendly chromatographic method to purify small regulatory RNAs

Project description:The discovery of the small regulatory RNA populations has changed our vision of cellular regulations. Indeed, loaded on Argonaute proteins they formed ribonucleoprotein complexes that target complementary sequences and achieved widespread silencing mechanisms conserved in most eukaryotes. The recent development of deep sequencing approaches highly contributed to their detection. Small RNA isolation form cells and/or tissues remains a crucial stage to generate robust and relevant sequencing data. In 2006, a novel strategy based on anion-exchange chromatography has been purposed as an alternative to the standard size-isolation purification procedure. However, the eventual biases of such a method have been poorly investigated. Moreover, this strategy not only relies on advanced technical skills and expensive material but is time consuming and requires an elevated starting biological material amount. Using bioinformatic comparative analysis of six independent small RNA-sequencing libraries of Drosophila ovaries, we here demonstrate that anion-exchange chromatography purification prior to small RNA extraction unbiasedly enriches datasets in bona fide reads (small regulatory RNA reads) and depletes endogenous contaminants (ribosomal RNAs and degradation products). The resulting increase of sequencing depth provides a major benefit to study rare populations. We then developed a fast and basic manual procedure to purify loaded small non coding RNAs using anion-exchange chromatography at the bench. We validated the efficiency of this new method and used this strategy to purify small RNAs from various tissues and organisms. We moreover determined that our manual purification increases the output of the previously described anion-exchange chromatography procedure. Comparison of small regulatory RNA populations obtained after three different small RNA purification procedures

2013-06-13 | E-GEOD-40748 | biostudies-arrayexpress

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

Project description:We investigated a pool of small RNAs derived from transposon Penelope to probe the evolution of small RNA pathways in response to the transposon challenge in natural (D. virilis) and experimentally induced (D. melanogaster) colonization processes. In both species, Penelope was predominantly targeted by endo-siRNAs rather than by piRNAs. Although we observed correlations between Penelope transcription and dysgenesis, we could not correlate differences in maternally deposited Penelope piRNAs with the sterility of progeny. Instead, we found that strains, which produced dysgenic progeny, differed in their production of piRNAs from clusters in sub-telomeric regions, possibly indicating that changes in the overall piRNA repertoire underlie dysgenesis. Considered together, our data reveal unexpected plasticity in small RNA pathways in germ cells, both in the character of their responses to invading transposons and in the piRNA clusters that define their ability to respond to mobile elements. Examination of total small RNA in 0-2h embryos, testes, ovaries and carcasses of several D. virilis strains and their hybrids; total small RNA and Ago2, Piwi, Aub and Ago3-associated small RNA in testes and ovaries of D. melanogaster.

2010-07-18 | E-GEOD-22067 | biostudies-arrayexpress

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