Isolation of dense DNA
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ABSTRACT:
PROVIDER: PRJEB78557 | ENA |
REPOSITORIES: ENA
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Project description:C3 glomerulopathy (C3G) is a rare disease resulting from dysregulation of the alternative pathway (AP) of complement. C3G includes C3 glomerulonephritis (C3GN) and dense deposit disease (DDD). Both C3GN and DDD are characterized by bright glomerular C3 staining on immunofluorescence studies. However, on electron microscopy, DDD is characterized by dense osmiophilic mesangial and intramembranous deposits along the glomerular basement membranes (GBM), while the deposits of C3GN are not dense. Why the deposits appear dense in DDD and not in C3GN is not known.We performed laser microdissection of glomeruli followed by mass spectrometry in 12 known cases of DDD and C3GN each to determine the proteomic profile and differences between C3GN and DDD.
2024-10-22 | PXD045319 | Pride
Project description:Objectives: MicroRNA (miRNA) can be released to the extracellular medium and participates in neuronal communication. We investigate the mechanisms of miRNA exocytosis by vesicle fusion as a neuromodulator in a manner that are disparate from silencing gene expression. Methods: Small RNA sequencing data of large dense-core vesicle were generated by next-generation sequencing (NGS) in triplicate using Illumina Hiseq 2500. Results: Large dense-core vesicles contain a variety of known and novel miRNAs inside including miR-375. Conclusion: miRNAs can be novel neuromodulators, which are stored in LDCVs and released by vesicle fusion by SNARE assembly and synaptotagmin-1
2017-01-01 | GSE84834 | GEO
Project description:We performed RNA-seq on RNA samples of dense and cystic organoids derived from mouse pituitary tissue
2019-06-16 | GSE116654 | GEO
Project description:Transcriptional profiling of dense and cystic organoids
| PRJNA479819 | ENA
Project description:Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for dense graph recovery. ELMM reconstructs the undirected graph of a regulatory network using empirical Bayes conditional independence testing with a heuristic relaxation of independence constraints in dense areas of the graph. This relaxation allows only one gene of a pair with a putative relation to be aware of the network connection, an approach that is aimed at easing multiple testing problems associated with recovering densely connected structures.Results: Using in silico data, we show that ELMM has better performance than commonly used network inference algorithms including PC Algorithm, GeneNet, and ARACNE. We also apply ELMM to reconstruct a network among 5,400 genes expressed in human lung airway epithelium of healthy nonsmokers, healthy smokers, and smokers with pulmonary diseases assayed using microarrays. The analysis identifies dense subnetworks that are consistent with known regulatory relationships in the lung airway and also suggests novel hub regulatory relationships among a number of genes that play roles in oxidative stress, wound response, and secretion.
2024-06-05 | GSE32030 | GEO
Project description:A mass spectrometry-based proteomics analysis was performed to study the proteome changes upon treatment with dense bodies derived from human cytomegalovirus infection.
2023-07-24 | PXD039032 | Pride
Project description:Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.
2024-02-22 | GSE256319 | GEO
Project description:Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.
2024-02-22 | GSE256318 | GEO
Project description:Toxoplasma gondii is an intracellular parasite that causes the disease toxoplasmosis in humans. It is a member of the phylum Apicomplexa that also includes significant human pathogens such as Plasmodium spp. and Cryptosporidium spp. causing malaria and diarrheal disease, respectively. These parasites use a programmed sequence of secretory events to find, invade, and then reengineer their host cells to enable parasite growth and proliferation. After invasion, Toxoplasma secretes proteins for host cell remodelling and manipulation from dense granules. The site(s) of dense granule exocytosis, however, has been unknown. In Toxoplasma gondii, small subapical annular structures that are embedded in the inner membrane complex have been observed, but the role or significance of these apical annuli to plasma membrane function has also been unknown. We have identified four integral membrane proteins of the plasma membrane that occur specifically at these apical annular sites. These proteins are an LMBR-domain containing protein TgLMBD3, and three SNARE proteins TgStxPM, TgNPSN, and TgSyp7. Using widefield-microscopy, we discovered that depletion of each of these proteins results in reduced secretion of dense granule proteins, implicating the apical annuli as a site of exocytosis in Toxoplasma. To further understand the role of these proteins and the impact of their depletion on the parasite, we performed whole-cell quantitative proteomics in control and knockdown cell lines. Several hundred proteins have been identified and quantified in three biological replicates for every knockdown cell line and the untreated control line. The majority of enriched proteins in the knockdown cell lines are those packaged in dense granules, indicating their failure to be secreted outside the cell. The apical annuli are therefore sites of SNARE-mediated exocytosis of dense granules in Toxoplasma.
2024-01-25 | PXD044588 | Pride
Project description:Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities, and adaptive potential. The origins of gene amplifications have remained elusive; however, one model suggests DNA rereplication could be a source of gene amplifications. The inability to determine which sequences are rereplicated and under what conditions have made it difficult to determine the validity of these models. Here we present RerepSeq, a technique that selectively fragments and enriches rereplicated DNA in preparation for next generation sequencing. RerepSeq is applicable to any species and can be utilized with low amounts of input DNA with rapid results. We validated RerepSeq by simulating DNA rereplication in yeast and human cells. Using RerepSeq, we demonstrate that rereplication induced in S. Cerevisiae by deregulated origin licensing is non-random and defined by broad domains that span multiple replication origins and topological boundaries.
2020-01-22 | GSE143572 | GEO