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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

ABSTRACT: Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

PROVIDER: PRJNA451503 | ENA |

REPOSITORIES: ENA

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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

Project description:Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

| PRJNA451502 | ENA

Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

Project description:Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

Project description:research was focus on the virus-derived sRNAs expression pattern in rice host or planthopper vector and host/vector gene expression pattern when infected with RSV

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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

Project description:research was focus on the virus-derived sRNAs expression pattern in rice host or planthopper vector and host/vector gene expression pattern when infected with RSV

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Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus.

Project description: Not available

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Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

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

2018-12-26 | GSE113555 | GEO

Characterize the regulon of 6C sRNA in Mycobacteria smegmatis

Project description:Purpose: The goals of this study are to identify the putative mRNA targets that are regulated by the 6C sRNA. We constuct an inducible vector to transiently overexpressed the 6C sRNA in M. smegmatis, and then we perform RNA-Seq to look for genes that are differicently expressed upon the over-expression of 6C sRNA, which we think these genes are the potential targets of the 6C sRNA.

2018-09-02 | GSE119364 | GEO

The rise and fall of billionaire siRNAs during reproductive development in rice [sRNA-seq]

Project description:RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNAdirected DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues.

2023-01-02 | GSE186406 | GEO

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (small RNA-seq)

Project description:Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype.

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Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

Project description:Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.

2020-01-13 | GSE142524 | GEO

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