Identification of urinary exosomal non-coding RNAs as novel biomarkers in chronic kidney disease
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Ion Torrent Proton
ORGANISM(S): Homo sapiens
SUBMITTER: Rimpi Khurana
PROVIDER: E-MTAB-5152 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. MicroRNAs are small nucleatides that function as regulators of gene expression in almost any biological process. However, few microRNAs are reported to have a role in the pathological process of OPLL. Therefore, we performed high-throughput microRNA sequencing and transcriptome sequencing of primary OPLL and PLL cells in order to decipher the interacting network of microRNAs in OPLL. MRNA and microRNA profiles were done using primary culture cells of human ossification of the posterior longitudinal ligament (OPLL) tissue and normal posterior longitudinal ligament (PLL) tissue.
2016-04-04 | E-GEOD-69787 | biostudies-arrayexpress
Project description:Especially in rare cancer types such as neuroendocrine breast cancer (NEBC), it is important to analyze the individual characteristics more deeply. NEBC itself is a highly heterogenous disease and no guidelines exist to date. To add another layer of information to understand the tumor characteristics better,we analyzed mRNA from two cancer patients to determine the signal transduction pathways and to identify possible contributions to a beneficial treatment. Among other procedures plasma samples (2 ml) from EDTA tubes were centrifuged at 16000g for 10 min at 4 °C and filtered via a 0.45 µm membrane to remove larger vesicles. The filtrate was used for the extraction of total exosomal RNA using an ExoRNeasy serum/plasma kit (QIAGEN, Germantown, USA) according to the manufacturer’s protocol. Purified exosomal RNA was quantified using an miRNA Qubit assay (Life Technologies, Carlsad, USA). The Ion AmpliSeq™ Transcriptome Human Gene Expression Research Panel was used to determine the expression of 20,802 genes including 18,574 coding genes and 2228 non-coding genes based on University of California Santa Cruz (UCSC) hg19 annotation.
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Project description:Background: Repair of DNA damage requires chromatin remodeling to permit removal of the lesions. How nucleosomes are remodelled to initiate repair of DNA damage remains largely unknown. Here, we describe how chromatin is altered during repair of UV-induced DNA damage at the level of the linear organisation of nucleosomes. Results: Using MNase-seq, we identified a subset of nucleosomes in the genome that are remodelled in UV-damaged wild-type yeast cells. We mapped the genomic location of these nucleosomes, showing that they contain the histone variant H2A.Z. The remodelling observed is consistent with histone exchange or eviction at these positions. This depends on the yeast SWI/SNF global genome nucleotide excision repair (GG-NER) chromatin-remodelling complex. Remarkably, we found that in the absence of DNA damage, the GG-NER complex occupies chromatin at nucleosome free regions separating adjacent nucleosomes. This establishes the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBS’s). We observed that these sites are frequently located precisely at certain boundary regions that delineate chromasomally interacting domains (CIDs). These boundaries define chromosomal domains of higher-order nucleosome-nucleosome interaction. We demonstrate that the GG-NER complex redistributes following remodelling of these nucleosomes after DNA damage taking up genomic positions located within the CIDs. This permits the efficient removal of DNA damage at these sites. Conclusions: We argue that organising DNA repair in the genome as described may define origins of DNA repair that greatly reduces the genomic search space for DNA damage recognition, thus ensuring the efficient repair of damage in chromatin.
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2019-12-01 | E-MTAB-6724 | biostudies-arrayexpress
Project description:Multiple system atrophy (MSA) is a fatal rapidly progressive Ia-synucleinopathy, characterized by prominent Ia-synuclein accumulation in oligodendrocytes. In this study we investigated miRNA expression in the substantia nigra and striatum of MSA transgenic mice (Tg(Plp1-SNCA)1Haa) and wild type controls. This forms part of a larger study in which we investigated miRNA-mRNA regulatory network in substantia nigra and striatum of MSA transgenic mice in pre-motor stage of neurodegenration.
2016-03-15 | E-MTAB-3993 | biostudies-arrayexpress
Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. Recently, disorders of metabolism are thought to be the center of many diseases such as OPLL. Advanced glycation end product (AGE) are accumulated in many extracellular matrixes such as ligament fibers, and it can functions as cellular signal through its receptor (RAGE), contributing to various events such as atherosclerosis or oxidative stress. However, its role in OPLL formation is not yet known. Therefore, we performed high-through-put RNA sequencing on primary posterior longitudinal ligament cells treated with different doses of AGEs (1µM, 5µM and negative control), with or without BMP2 (1µM). mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1µM AGE-BSA, 5µM AGE-BSA, 1µM AGE-BSA with BMP2, 5µM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton
2016-02-16 | E-GEOD-65952 | biostudies-arrayexpress
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