Small RNA sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29502 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR3307962.fastq.gz | Fastqsanger.gz | |||
| ERR3307957.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear RNAi Argonaute HRDE-1. Furthermore, HRDE-1 also localizes to SIMR foci, dependent on HRDE-2, but only in its small RNA unbound state. This germ granule localization is critical to promote the small RNA binding specificity of HRDE-1 and, in the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that HRDE-2 is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.
2023-07-27 | MSV000092546 | MassIVE
Project description:Gene silencing in parasitic nematodes was achieved by infecting Nippostrongylus with lentivirus designed to produce small RNAs to silence specific genes. Small RNA sequencing was used to investigate production of small silencing RNAs in infected nematodes
2020-11-28 | GSE162219 | GEO
Project description:MiRNAs and possibly the recently discovered piRNAs can function in reversible gene silencing. In meiosis, transcriptional silencing of the XY bivalent and the late pairing regions of autosomes is a necessary event and defects in these processes lead to infertility. The exact mechanisms of meiotic gene silencing are not well understood but it is thought that some RNA component might be involved at least in the XY transcriptional silencing, similar to Xist silencing of the X chromosome in females. We wanted to investigate if small RNA species are present in the meiotic nucleus and, if so, to determine their localization pattern. We found both miRNAs and piRNAs in the nucleus of spermatogenic cells. In Sertoli cells, miRNAs and piRNAs are localized to the fibrillogranular compartment of the nucleolus, while in meiotic cells they are found mainly in the XY-associated dense body but also are associated with chromosome cores, telomerers and the sex chromatin. Interestingly, in MIWI null male mice, the nucleolar localization of miRNAs is decreased while the localization of piRNAs is diminished. However, the meiotic localization of these two components is not affected. These data suggest that small RNA species might have different roles during different stages of male gametogenesis and undergo differential regulation. Based on the localization of miRNAs and piRNAs in the male-specific, XY-associated dense body, it is probable that at least some are involved in the silencing of the XY bivalent. Others might be involved in translational repression of transcripts used in later stages of spermiogenesis when transcription is halted. Keywords: total RNA direct hybridization
2008-02-22 | GSE8118 | GEO
Project description:Small RNA sequencing during salinity stress response in chickpea (small RNA-Seq)
| PRJNA842021 | ENA
Project description:Small RNA (sRNA) sequencing data from pre-meiotic and meiotic anthers of Asparagus
| PRJNA449052 | ENA
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.
2009-12-31 | E-GEOD-17339 | biostudies-arrayexpress
Project description:The 35S::GFP fluorescence was silenced 6-day after infiltration to Nicotiana benthamiana leaves due to the post-transcriptional gene silencing, but became stable by adding the viral suppressor 2b which repressed RNA silencing in plants. We performed the small RNA high throughput sequencing to test whether WUS can inhibit 2b functions in repressing plant RNA silencing.
2021-02-22 | GSE128863 | GEO
Project description:Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of A. officinalis (Asparagus) anthers.
2018-07-07 | GSE112800 | GEO
Project description:Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of H. lilioasphodelus (Daylily) anthers.
2018-07-07 | GSE112799 | GEO
Project description:RNA silencing is a conserved mechanism in eukaryotes and is involved in development, heterochromatin maintenance and defense against viruses. In plants, ARGONAUTE1 (AGO1) protein plays a central role in both microRNA (miRNA) and small interfering RNA (siRNA)-directed silencing and its expression is regulated at multiple levels. Here, we report that the F-box protein FBW2 targets proteolysis of AGO1 by a CDC48-mediated mechanism. We found that FBW2 assembles an SCF complex that recognizes the MID-PIWI domain of AGO1 and requires its C-terminal domain containing a GW motif for AGO1 turnover. We showed that FBW2 has a preference for the unloaded and for some mutated forms of AGO1 protein. While FBW2 loss of function does not lead to strong growth or developmental defects, it significantly increases RNA silencing activity. Interestingly, under conditions in which small RNA production or accumulation is affected, the failure to degrade AGO1 in fbw2 mutants becomes more deleterious for the plant. Hence, we showed that the non-degradable AGO1 protein assembles high molecular complexes and binds illegitimate small RNA leading to the cleavage of new target genes that belong to stress responses and cellular metabolic processes. Therefore, the control of AGO1 homeostasis by ubiquitin ligases, plays an important quality control to avoid off-target cleavage.
2022-04-01 | PXD024840 | Pride