New Insights into the Complex Pathophysiology of Restless Legs Syndrome from a Transcriptome Analysis of mRNAs
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Genomix4Life Genomix4Life
PROVIDER: E-MTAB-13155 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This experiment captures the expression of genes between two sites of human cartilage within the same patients to allow investigation of genomic responses to damage during osteoarthritis. Eight patients with symptomatic OA undergoing total knee replacement (n=8, age range 65-79 years, mean age 70.3) were used in this study. Cartilage from paired osteochondral samples were isolated from the intact PLC (posterior lateral condyle) and the damaged DMC (distal medial condyle) for RNA-seq analysis.
2016-04-06 | E-MTAB-4304 | biostudies-arrayexpress
Project description:Background: Despite significant improvements in short-term kidney transplant survival, comparable increases in 5 and 10-year outcomes have not been achieved. Chronic allograft nephropathy (CAN) is a major cause of late graft loss. Toxic nephropathy and inadequate long-term immunosuppression are possible factors. We performed a randomized prospective trial comparing calcineurin inhibitor (CNI)-free to CNI-based immunosuppression to determine the impact on renal function, structure, and gene expression. Methods: Sixty-one kidney recipients received mycophenolate mofetil (MMF), and prednisone (P). Randomized patients received concentration-controlled sirolimus or cyclosporine. Two years post-transplant 55 patients underwent renal function studies, 48 (87%) underwent transplant biopsies; all classified by Banff scoring and 41 by DNA microarrays. Findings: Comparing sirolimus/MMF/P to cyclosporine/MMF/P at two years, there was a significantly lower serum creatinine (1.35 vs. 1.81 mg/dl; p=0.008), significantly higher Cockroft-Gault glomerular filtration rate (GFR) (80.4 vs. 63.4 cc/min; p=0.008), iothalamate GFR (60.6 vs. 49.2 cc/min; p= 0.018), and Banff 0 (normal) biopsies (66.6 vs. 20.8%; p=0.013). Regression analysis of calculated GFR’s from 1 to 36 months yielded a positive slope for sirolimus of 3.36 ml/min/year, and a negative slope for cyclosporine of –1.58 ml/min/year (p=0.008). Gene expression profiles of kidney biopsies with higher Banff CAN scores confirmed significant up regulation of genes responsible for immune/inflammation and fibrosis/tissue remodeling. Interpretation: At two years the sirolimus-treated patients have better renal transplant function, a diminished prevalence of CAN, and down regulated expression of genes responsible for the progression of CAN. All may provide for an alternative natural history with improved graft survival. Keywords = Cyclosporine Keywords = Sirolimus Keywords = Transplantation Keywords = DNA microarrays Keywords = calcineurin inhibitors Keywords: parallel sample. This dataset is part of the TransQST collection.
2004-09-23 | E-GEOD-1743 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:Postural orthostatic tachycardia syndrome (POTS) is a cardiovascular autonomic disorder leading to debilitating symptoms and the therapeutic alternatives are limited. Proteomics is a large-scale study of proteins that enables a systematic unbiased view on disease and health, allowing stratification on patients based on their protein background. We aimed to explore proteins that may be related with the putative etiology of POTS compared with healthy controls using a highly powerful targeted proteomic mass spectrometry technique. We aimed to explore proteins that may be related with the putative etiology of POTS compared with healthy controls using a highly powerful targeted proteomic mass spectrometry technique.
2022-11-24 | PXD031458 | Pride
Project description:ADPKD (Autosomal dominant polycystic kidney disease) is the most common inherited disorders and is characterized by growth of numerous cysts filled with fluid in the kidneys. Ultimately, it leads to kidney failure. The mutations of PKD1 and PKD2 account for approximately 85 and 15 percent of ADPKD, respectively. However, the mechanisms related to genetic mutation of PKD1 and PKD2 are still unclear. To investigate altered gene expression levels, Affymetrix microarray was performed using the kidney tissue from normal and ADPKD patients. Total RNAs were isolated from kidney of human normal (49 years old/ male) and ADPKD patients (62 years old/ male, 67 years old/ male) using NucleoSpin® RNA Kit (MACHEREY-NAGEL) according to the manufacturer’s instructions. We used tha Affymetrix GeneChip Human Gene 1.0 ST Array. Per RNA sample, 300 ng was used as the input into the Affymetrix procedure as recommended by the manufacturer's protocol.
2012-02-16 | E-GEOD-35831 | biostudies-arrayexpress
Project description:The rapeseed crop (Brassica napus) is valued mainly for animal feed, food oil and biofuel production. This plant is particularly susceptible to many pathogens like parasitic plants, fungi or animals attacking aerial or root parts. Conventional plant protection products, used intensively in agriculture, have a negative impact on the environment (air and water quality, biodiversity, etc.) as well as on human health. There is therefore a growing demand for the development of new, more planet-friendly alternative protection methods such as biocontrol compounds. Natural rhamnolipids (RLs) can be used as elicitors of plant defense mechanisms. Indeed, these glycolipids, from bacteria secretome, are biodegradable, non-toxic and they are known for their stimulating and protective effects, in particular on rapeseed against filamentous fungi. Characterizing the organ responsiveness to defense stimulating compounds like RLs is missing. This analysis is crucial in the frame of optimizing the effectiveness of RLs against various diseases. A TMT labeling of the proteins extracted from the shoots and roots of B. napus has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several protein families possibly involved in the differential responses observed in shoots and roots of rapeseed upon RLs treatment. In particular, quantitative proteomic analysis highlighted differential accumulation of parietal and cytoplasmic defense or stress proteins in response to treatments with RLs with a clear effect of the type of application (foliar spraying or root absorption). These results must be considered for further use of RLs to fight specific rapeseed pathogens.
2023-01-24 | PXD038531 | Pride
Project description:Articular cartilage is deprived of blood vessels and nerves, and the only cells residing in this tissue are chondrocytes. The molecular properties of the articular cartilage and the architecture of the extracellular matrix demonstrate a complex structure that differentiates on the depth of tissue. Osteoarthritis (OA) is a degenerative joint disease, the most common form of arthritis, affecting the whole joint. It is associated with ageing and affects the joints that have been continually stressed throughout life including the knees, hips, fingers, and lower spine region. OA is a multifactorial condition of joint characterised by articular cartilage loss, subchondral bone sclerosis, and inflammation leading to progressive joint degradation, structural alterations, loss of mobility and pain. Articular cartilage biology is well studied with a focus on musculoskeletal diseases and cartilage development. However, there are relatively few studies focusing on zonal changes in the cartilage during osteoarthritis.
2022-05-19 | PXD029116 | Pride
Project description:Nocturnal home hemodialysis (NHD) [5 â 6 times a week, 6-8 hours per session] augments uremia clearance and is associated with an increase in hemoglobin level. We have used microarray to have a global image of the changes at the gene expression. Experiment Overall Design: Sixteen stable end-stage renal disease patients (age: 47 ñ 2 years; 9M) [mean ñ SEM] were studied. Total RNA (TRNA) was isolated from whole blood before and after 3 months of established NHD. Gene expression before and after NHD was acquired through hybridizations on Human HG-U133_PLUS2 GeneChip and genes with differential gene expression were identified.
2009-01-13 | E-GEOD-11227 | biostudies-arrayexpress
Project description:Left-right asymmetry is a basic character of aging brain; however, the molecular foundation of the left-right asymmetry remains unclear. The morphology, physiology and behavior of rhesus aging are obviously similar to human aging, but the aging-rate of rhesus is roughly three times as fast as human, in which the underlying mechanism needs further investigation. By using of 6-plex tandem mass tag (TMT) labeling, we presented a high throughput quantitative proteomics analysis to 6 group hippocampal samples including left and right hippocampus from 3 years, 6 years and 20 years old rhesus. Our data identified 3391 high-confidence proteins. After screening, we found 340 aging-related proteins of left hippocampus and 334 aging-related proteins of right hippocampus, in which there were 114 overlap proteins. Furthermore, the aging-related proteome of left rhesus hippocampus aging was compared with human aging-related proteome of left hippocampus that was reported by our lab previously. As the results show, we discovered 446 aging-related proteins in rhesus and 830 aging-related proteins in human with an overlap of 106 proteins.
2020-01-23 | PXD011398 | Pride
Project description:Although the COVID-19 pandemic has ended, it is important to understand the pathology of severe SARS-CoV-2 infection associated with respiratory failure and high mortality. In this study, a proteomics approach using nano-HPLC-MS/MS (QExactive HF) was used to compare the plasma proteome of COVID-19 survivors (COVID-19; n=10) and deceased individuals (CovDeath; n=10) with that of healthy individuals (Ctr; n=10). The effects of SARS-CoV-2 infection on the alteration of plasma proteins by lipid peroxidation products such as 4-hydroxynonenal (4-HNE), malondialdehyde (MDA) and 15-deoxy-12,14-prostaglandin J2 (15d-PGJ2) were also examined. The results suggest that the development of COVID-19 strongly alters the expression of proteins involved in the regulation of exocytosis and platelet degranulation. These changes were most pronounced in the CovDeath group. In addition, a significant increase in proteins modified with reactive aldehydes was observed in all patients. In the COVID-19 and CovDeath groups, the levels of 4-HNE adducts increased 2- and 3-fold, respectively, whereas MDA adducts increased 7- and 2.5-fold, respectively. Signaling kinases and proinflammatory proteins were particularly affected by these modifications, and the amount of 4-HNE modifications confirmed previous findings on the relevance of 4-HNE in disease pathogenesis and lethal outcome. Protein adducts with 15d-PGJ2 were increased 2.5-fold in COVID-19 patients, including modifications of proteins such as p53 and STAT3, whereas CovDeath showed a decrease of approximately 60% compared with Ctr. It can be assumed that the observed changes in protein expression and modification in COVID-19 are unlikely to be used as prognostic biomarkers because they are also present in the other inflammatory diseases. However, larger studies may prove that the extent and the nature of protein modifications in plasma may be a predictor of the course of SARS-CoV-2 infection.
2023-10-24 | PXD044040 | Pride