Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13763500.fastq.gz | Fastqsanger.gz | |||
| ERR13763501.fastq.gz | Fastqsanger.gz | |||
| ERR13763502.fastq.gz | Fastqsanger.gz | |||
| ERR13763503.fastq.gz | Fastqsanger.gz | |||
| ERR13763499_1.fastq.gz | Fastqsanger.gz |
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Project description:RNAi expression experiments on Illumina BeadChip
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Project description:Floral bicolor pigmentation is caused by naturally occurring RNA interference (RNAi) in some cultivars of petunia and dahlia. In both plants, the chalcone synthase gene is highly expressed only in the pigmented region of bicolor petals. However, it remains unknown why RNAi is induced only in the unpigmented region. To elucidate the mechanism of this bicolor pattern formation, we examined the dicing activity of Dicer-like 4 (DCL4), which produces small interfering RNAs essential for RNAi. We showed that the crude extract in the pigmented region inhibits DCL4 activity, but not when flavonoids were depleted from the extract. Moreover, we showed the inhibitory activity was associated with flavonoid aglycons. The in vivo dicing activities were detected in the intact protoplasts prepared from the unpigmented region but not from the pigmented region. These results suggest that in the unpigmented region, flavonoids that inhibit DCL4 are not synthesized, and RNAi is maintained, whereas in the pigmented region, DCL4 (RNAi) is inhibited by flavonoids and anthocyanin biosynthesis is maintained. The results of small RNA-seq analyses of bicolor petals and exogenous flavonoid application experiments support this conclusion. Therefore, a clear bicolor pattern is generated by the bidirectional feedforward mechanism of antagonizing DCL4 and flavonoids.
2025-07-09 | GSE302198 | GEO
Project description:Complex lipid metabolism plays a crucial role in regulating aging. We recently discovered that the phospholipid bis(monoacylglycero)phosphate (BMP) increases in aged human muscles and many mouse tissues. The phospholipase PLA2G15 is reportedly involved in BMP synthesis, however, its specific role in aging remains unknown. To elucidate the role of PLA2G15 in aging, we used C. elegans as a model. When silencing plag-15, the predicted worm orthologue of PLA2G15, we observed improved healthspan and lifespan extension. Semi-targeted lipidomics highlighted that instead of changes related to BMP, plag-15 RNAi led to lower levels of lysophosphatidic acid, lysophosphatidylcholine and lysophosphatidylethanolamine. Transcriptome-guided epistasis experiments identified that the lifespan extension of plag-15 RNAi worms is regulated by transcription factors hlh-30 and elt-3, and lysosomal vitamin B12 transporter pmp-5 (human TFEB, GATA, and ABCD4 respectively). Overall, we conclude that targeting phospholipid remodeling through plag-15 could be a promising strategy to promote healthy aging.
2025-06-19 | MTBLS12324 | MetaboLights
Project description:The comparison of trancriptomes was part of the study by Pfender, Kuznetsov, Pasternak et al, titled: "Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes". The goal was to check if the oocytes cultured in vitro in follicles (for RNAi studies) correspond to real gametes obtained directly from mice (in vivo). Apart from functional experiments showing that they can be fertilized and develop into an embryo, we also compared transcriptomes of those oocytes.
2015-07-06 | GSE68150 | GEO
Project description:Transcriptional profiling comparing adult wild-type indirect flight muscle (IFM) with wild-type leg muscle and salm RNAi IFM (Mef2-GAL4, UASsalmIR). We used 2 different salm hairpin constructs for the experiments, TF3029 and TF101052, both available from the VDRC Drosophila stock centre.
2011-03-01 | GSE27502 | GEO
Project description:Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage. Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays. Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.
2020-12-01 | GSE119493 | GEO
Project description:Nardilysin (NRDc), a metalloendopeptidase of the M16 family, has been reported to promote the ectodomain shedding and resulting activation of various growth factors and cytokines, but its role in cancer biology have not been elucidated. Microarray experiments were performed to analyze the chnages of gene expression profiles after knockdown of NRDc by microRNA (miR)-based RNA interference (RNAi). RNAi experiments were perfomed using BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP (Invitrogen). TMK-1 cells stably expressing conrol or NRDc-targeting miR vector were established.
2011-05-16 | E-GEOD-29144 | biostudies-arrayexpress
Project description:Aedes aegypti mosquitoes vector several arboviruses of global health significance, including dengue viruses and chikungunya virus. RNA interference (RNAi) plays an important role in antiviral immunity, gene regulation and protection from transposable elements. Double-stranded RNA binding proteins (dsRBPs) are important for efficient RNAi; in Drosophila functional specialization of the miRNA, endo-siRNA and exo-siRNA pathway is aided by the dsRBPs Loqs-PB, Loqs-PD and R2D2, respectively. However, this functional specialization has not been investigated in other dipterans. Characterization of the gene structure, expression pattern and interactions with other RNAi/miRNA components revealed that mosquito Loqs/R3D1 isoform -PA, but not -PB interacted readily with both AeAGO1 and AeAGO2. This interaction was mapped to a 32 a.a. region predicted to be structurally similar to the unique 22 a.a. tail of Drosophila Loqs-PD. No -PD isoforms could be detected in Ae. aegypti; analysis of other dipteran genomes demonstrated that this isoform is not conserved outside of Drosophila. Overexpression experiments indicated that Loqs/R3D1-PA participates in endo-siRNA, but not exo-siRNA based silencing. We conclude that the functional specialization of Loqs-PD in Drosophila is a recently derived trait, and that in other dipterans, including the medically important mosquitoes, Loqs/R3D1-A participates in both the miRNA and endo-siRNA based pathways.
2015-04-08 | GSE65070 | GEO
Project description:Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in C. elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4. The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1. Together, our results identify additional components of the RNAi inheritance machinery whose sequence conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.
2017-06-20 | GSE92840 | GEO