Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of urinary exosomal non-coding RNAs as novel biomarkers in chronic kidney disease

ABSTRACT: We aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of Chronic Kidney Disease (CKD) for this, we examined 15 exosomal ncRNA profiles in urine samples from CKD patients from four different stages (I, II, III and IV) and compared them to 10 healthy controls. We identified a significant number of novel, differentially expressed ncRNAs in CKD patients compared to healthy, which might be employed as early diagnostic markers in CKD in the future.

INSTRUMENT(S): Ion Torrent Proton

ORGANISM(S): Homo sapiens

SUBMITTER: Rimpi Khurana

PROVIDER: E-MTAB-5152 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of neuromuscular junction during degeneration and regeneration of axon terminal

Project description:The neuromuscular junction (NMJ) is a specialized tripartite synapse composed of the motor axon terminal, covered by perisynaptic Schwann cells (PSCs), and the muscle fibre, separated by a basal lamina. It is exposed to different kind of injures such as mechanical traumas, pathogens including neurotoxins, and neuromuscular diseases such as amyotrophic lateral sclerosis and immune-mediated disorders, and has retained throughout vertebrate evolution an intrinsic ability for repair and regeneration, at variance from central synapses1. Following peripheral nerve injury, an intense but poorly defined crosstalk takes place at the NMJ among its components, functional to nerve terminal regeneration. To identify crucial factors released by PSCs and the muscle to induce nerve regrowth, we performed a transcriptome analysis of the NMJ at different time points after injection of -latrotoxin, a presynaptic neurotoxin isolated from the venom of the black widow spider. This toxin is a simple and controlled method to induce an acute, localized and reversible nerve terminal degeneration not blurred by inflammation, and can help to identify molecules involved in the intra- and inter-cellular signalling governing NMJ regeneration.

2017-05-30 | E-MTAB-5730 | biostudies-arrayexpress

RNA-Seq of Brachypodium distachyon callus treated with methyl-jasmonate

Project description:The aim was to determine the changes in cell wall composition and transcriptome changes following treatment with the stress hormone precursor methyl jasmonate (MeJA) in the model grass Brachypodium distachyon. The correlation between transcript changes and cell wall composition changes allowed identification of candidate genes responsible for grass-specific features of the cell wall that are specifically changed in response to MeJA.

2017-09-04 | E-MTAB-5413 | biostudies-arrayexpress

Transcriptome and Micronome analysis of OPLL

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

Extensive tumour profiling in primary neuroendocrine breast cancer cases as a role model for personalized treatment in rare and aggressive cancer types

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.

2022-05-19 | E-MTAB-11703 | biostudies-arrayexpress

The yeast GG-NER complex evicts histone H2A.Z-containing barrier nucleosomes from CID boundaries during DNA repair

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.

2018-12-06 | E-MTAB-6569 | biostudies-arrayexpress

Lactate sensing drives fungal immune evasion

Project description:Experiment Description RNA sequencing was performed on Candida albicans wild type cells (SC5314) grown to exponential phase on YNB Lactate, YNB Glucose, or YNB Glucose plus Lactate, and compared to exponential Candida albicans crz1 cells grown on YNB Glucose or YNB Glucose plus Lactate. Three independent experiments were performed.

2016-10-03 | E-MTAB-4579 | biostudies-arrayexpress

RNA-seq of THP-1-derived macrophages infected with R. conorii and R. montanensis (1 hpi) against uninfected cells.

Project description:R. conorii (pathogenic) and R. montanensis (non-pathogenic) display opposite survival versus death phenotypes in macrophage-like cells, respectively. We herein employed a global transcriptomic profiling of host responses to infection (1hpi) of human THP-1 macrophages with R. conorii and R. montanensis. Shortly, total RNA was harvested from uninfected, R. conorii- and R. montanensis-infected THP-1 macrophages, DNA was removed from RNA purification (DNAse treatment), ribosomal RNA was depleted and cDNA libraries were constructed. The samples were sequenced using an Ion Proton V2 chip on Ion Chef Instrument. The programmes Cufflinks and Cuffmerge were used to map transcripts and calculate gene expression, and Cuffdiff was used to calculate which samples had genes, which were statistically significantly differentially expressed between conditions.

2019-12-01 | E-MTAB-6724 | biostudies-arrayexpress

microRNA profiling by high-throughput sequencing in the substantia nigra and striatum of Multiple System Atrophy (MSA) transgenic mice and wild type controls

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

Transcriptome analysis of Advanced glycation end products treated ligament cells

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 (1ÂµM, 5ÂµM and negative control), with or without BMP2 (1ÂµM). mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1ÂµM AGE-BSA, 5ÂµM AGE-BSA, 1ÂµM AGE-BSA with BMP2, 5ÂµM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton

2016-02-16 | E-GEOD-65952 | biostudies-arrayexpress

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - II

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using calibrated RNAPII-ChIP-seq, we determined the transcription profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were crosslinked at the beginning (t0) or the end (t9) of a 9h shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before crosslinking.

2024-06-30 | E-MTAB-13714 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data