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Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of single-stranded (SS) spike-in piRNA-like molecules in smallRNA-seq

ABSTRACT: Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of single-stranded (SS) spike-in piRNA-like molecules in smallRNA-seq

PROVIDER: PRJEB41397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4845106.fastq.gz	Fastqsanger.gz
	ERR4845107.fastq.gz	Fastqsanger.gz
	ERR4845108.fastq.gz	Fastqsanger.gz

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Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of single-stranded (SS) spike-in piRNA-like molecules in smallRNA-seq

Project description:For the evaluation of \\"WIND: A Workflow for pIRNAs aNd beyonD\\" performance and the transcriptomic approach on small-RNA identification, and particularly on piRNAs, a synthetic set of 4 piRNA-like molecules was used. Two non-methylated (SS-22 and SS-28) and two methylated (mSS-22 and mSS-28) of two different lengths (22 nt and 28 nt) were included. Spike-ins were chemically synthesised at Exiqon, the pool of 4 molecules was used at three different concentrations, with a final amount of 0.3 x 10^9 (dil_A), 0.3 x 10^10 (dil_B) and 0.3 x 10^11 (dil_C) molecules/ug of RNA. Library preparation and sequencing were done as previously described in Sellitto et al 2019 (doi: https://doi.org/10.3390/cells8111390)

2020-11-25 | E-MTAB-9772 | biostudies-arrayexpress

Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA in mouse samples

Project description:For the evaluation of "WIND: A Workflow for pIRNAs aNd beyonD" performance and the transcriptomic approach on small-RNA identification, and particularly on piRNAs, two mouse Adult Cardiomyocytes (aCMs) were used.

2020-11-28 | E-MTAB-9866 | biostudies-arrayexpress

Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA molecules in small RNA-seq

Project description:WIND: A Workflow for pIRNAs aNd beyonD, for the evaluation of the performance in piRNAs high expression and low expression conditions, we used Human Testis RNAs (BioChain Institute Inc, Newark, CA, USA) and COLO 205 cell line RNAs (samples are available on ArrayExpress (E-MTAB-8115: Non_treated_Testis_1 and Non_treated_COLO205_1, Non_treated_COLO205_2, Non_treated_COLO205_3).

2020-11-25 | E-MTAB-9782 | biostudies-arrayexpress

Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA in mouse samples

Project description:Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA in mouse samples

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Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA molecules in small RNA-seq

Project description:Monitor the efficiency of "WIND: A Workflow for pIRNAs aNd beyonD" for the identification of piRNA molecules in small RNA-seq

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Streptomyces sp. SS strain:SS

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Mitochondrial protein interaction landscape of SS-31

Project description:SS-31 is a synthetic peptide that improves mitochondrial function and is currently undergoing clinical trials for treatments of heart failure, primary mitochondrial myopathy, and other mitochondrial diseases. SS-31 interacts with cardiolipin which is abundant in the inner mitochondrial membrane, but mechanistic details of its pharmacological effects are unknown. Here we apply a chemical cross-linking/mass spectrometry method to provide direct evidence for specific interactions between SS-31 and mitochondrial proteins. The identified SS-31 interactors are functional components in ATP production and 2-oxoglutarate metabolism and signaling, consistent with improved mitochondrial function resultant from SS-31 treatment. These results offer a glimpse of the protein interaction landscape of SS-31 and provide mechanistic insight relevant to SS-31 mitochondrial therapy

2020-06-12 | PXD019484 | Pride

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Project description:Sjogren's syndrome (SS) dry eye is a chronic autoimmune eyedisease driven by T helper 17 (Th17)cells. S100A8/A9 has emerged as an important proinflammatory alarmin in variousautoimmune and inflammatory diseases. However, the role of S100A8/A9 in the pathogenesis of SS dry eye remains unexplored. Here,we show that the expression levels of S100A8/A9 were elevated in peripheral blood mononuclear cells (PBMCs) of patients with SS dry eye, as well as the lacrimal glands (LGs) of SS dry eye mice. The administration of paquinimod, a specific inhibitor of S100A8/A9, could alleviate the progression of SS dry eye with significant reduction of Th17 cell frequency in LGs, spleen and lymph nodes of SS dry eye mice.Further experiment revealed that S100A8/A9 did not directly affect Th17 generation and function, but upregulated the expression of MHCIl andI123a in DCs to augment Th17 cell response through a Acod1/STAT3-dependent signaling pathway in the context of SS dry eye. Together,these findings unveiled the key role of S100A8/A9 in the pathogenesis of SS dry eye and suggested a potential therapeutic avenue for SS dry eyeand otherTh7 cell-related autoimmune disorders.

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SS-31 protects against paraquat-induced lung injury and fibrosis via inhibition of the MAPK signal pathway

Project description:Aims: To explore the therapeutic effect of SS-31 on lung injury and lung fibrosis caused by paraquat (PQ). Methods: In vivo experiments involved the intraperitoneal injection of PQ solution into C57BL/6 mice to induce lung injury and fibrosis. Subsequently, SS-31 solution was administered intraperitoneally on a daily basis to investigate its protective effects against PQ-induced lung injury and fibrosis. In vitro use of PQ caused inflammatory responses in A549 cell line, and the therapeutic effects of SS-31 were explored by treatment with different concentrations of SS-31 in A549. The SS-31 pathway of action was explored and validated by RNA sequencing. Results: In vivo, SS-31 reduced PQ-induced mortality, acute lung injury, lung fibrosis and apoptosis in mice. The same results were obtained iin vitro experiments. SS-31 was found to inhibit the MAPK pathway by RNA sequencing. The mechanism was further validated by verifying MAPK pathway proteins and applying MAPK pathway agonists. Innovation and Conclusion: In vivo and in vitro experiments demonstrated that SS-31 reduces lung injury and fibrosis induced by PQ. It works through inhibition of the MAPK signaling pathway.

2026-03-15 | GSE261616 | GEO

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