RNA-seq of human hypertrophic scar fibroblast cell treated with pcolce siRNA against untreated controls
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Xiaolu Huang
PROVIDER: E-MTAB-9472 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:human hypertrophic scar fibroblast cell treated with fkbp10 siRNA and control siRNA for 48 hours
2020-08-26 | E-MTAB-9471 | biostudies-arrayexpress
Project description:Hypertrophic scar (HTS) formation is characterized by exuberant fibroproliferation for reasons that remain poorly understood1. One important but often overlooked component of wound repair is mechanical force, which regulates reciprocal cell-matrix interactions through focal adhesion components including focal adhesion kinase (FAK)1,2. Here we report that FAK is activated following cutaneous injury and that this activation is potentiated by mechanical loading. Transgenic mice lacking fibroblast-specific FAK exhibit significantly less fibrosis in a preclinical model of HTS formation. Inflammatory pathways involving monocyte chemoattractant protein-1 (MCP-1), a chemokine highly implicated in human skin fibrosis3, are triggered following FAK activation, mechanistically linking physical force to fibrosis. Further, small molecule inhibition of FAK effectively abrogates fibroproliferative mechanisms in human cells and significantly reduces scar formation in vivo. Collectively, these findings establish a molecular basis for HTS formation based on the mechanical activation of fibroblast-specific FAK and demonstrate the therapeutic potential of targeted mechanomodulatory strategies. Wildtype murine tissue was harvested at either day 6 or 14 post-injury following 48 hours or 10 days of mechanical loading, respectively (n=4 mice per group per time point). Murine RNA was isolated, labeled, and hybridized to the GeneChip microarray according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA). Each gene in the microarray was represented by 20 oligonucleotide pairs, with each pair consisting of an oligonucleotide perfectly matched to the cDNA sequence, and a second oligonucleotide containing a single base mismatch. Raw microarray data (sample intensity files) were processed using GeneSpring GX 11.0 (Agilent Technologies Inc., Santa Clara, CA, USA).
2011-01-14 | E-GEOD-26390 | biostudies-arrayexpress
Project description:RNA-seq of human hypertrophic scar fibroblast cell treated with pcolce siRNA against untreated controls
| PRJEB39958 | ENA
Project description:The goal was to obtain expression data from the deep cones in early human hypertrophic scars to be used to confirm expression data obtained in a porcine model. Three samples of early human hypertrophic scar were obtained and processed with the Affymetrix Human GeneChip® Human Genome U133 plus 2.0. Sample demographics were Black 2, White 1; upper extremity 2, neck 1; times since injury 6.7 months and 10.8 months; and patient ages were 19 and 54.
2011-12-31 | E-GEOD-26213 | biostudies-arrayexpress
Project description:Urea can serve as nitrogen source for coral holobionts and plays a cruscial role in coral calcification, although the degradation of urea by coral symbionts is not fully understood. In this study, we investigated the urea utilized pathway and the responses of the Symbiodiniaceae family to urea under high temperature conditions. Genome screening revealed that all Symbiodiniaceae species contain the urease (URE) and DUR2 subunit of urea amidolyase (UAD) system. However, only three speciesCladocopium goreaui, Cladopium c92, and Symbiodinium pilosum possess a complete UAD system, including both DUR1 and DUR2. Phylogentic analyses revealed that the UAD system in Symbiodiniaceae clusters more closely with symbiotic bacteria, indicating that horizontal gene transfer of UAD system has occured in coral symbionts. Physiology analysis showed that the symbiodiniacean species Cladocopium goreaui, which containing both URE and UAD, grew better under urea than ammonium conditions, as indicated by higher maximum specific growth rates. Furthermore, most genes of Symbiodiniaceae involved in urea utilization appeared to be stable under various conditions such as heat stress (HS), low light density, and nitrogen deficiency, wheras in ammonium and nitrate transporters were significantly regulated. These relatively stable molecular regulatory properties support sustained urea absorption by Symbiodiniaceae, as evidenced by an increase in δ15N2-urea absorption and the decreases in δ5N-NO3-, and δ15N-NH4+ from cultural environment to Symbiodiniaceae under HS conditions. Token together, this study reveals two distinct urea utilization systems in coral ecosystem and highlights the importance of the urea cycle in coral symbionts when facing fluctuating nitrogen environment in future warming ocean.
2024-09-27 | PXD056312 | Pride
Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.
2016-10-10 | PXD004039 | Pride
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:To test the ability of the Automated Spatially Targeted Optical Micro Proteomics (AutoSTOMP) protocol to selectively biotinylate structures of interest within tissue sections we first examined a rat myocardial infarction model. In this model, trauma caused by ligation and infiltrating immune cells causes fibroblast activation and deposition of scar tissue that ultimately impairs cardiac function. Macrophages are thought to play a role in inflammatory regulation and damaged cell turnover in the tissue. We decide to grab the proteome of the macrophage rich regions.
2021-08-10 | PXD026818 | Pride
Project description:Longitudinal bone growth depends upon the execution of an intricate series of cellular activities by epiphyseal growth plate chondrocytes. In order to better understand these coordinated events, microarray analysis was used to compare gene expression in chondrocytes isolated from the proliferative and hypertrophic zones of the avian growth plate. In this experiment we compared pooled samples of proliferative and hypertrophic chondrocytes isolated from the chick growth plate. The expression of 745 genes was found to differ 3-fold or greater at the 0.05 level of probability. Experiment Overall Design: We examined 8 samples using arrays: 4 from proliferative and 4 from hypertrophic chondrocytes.
2009-10-23 | E-GEOD-18568 | biostudies-arrayexpress
Project description:To explore the pathogenesis of myocardial hypertrophy, Proteomic Analysis was performed to identify the differentially expressed proteins in the human myocardial tissues of non-hypertrophic control and myocardial hypertrophy patients. We used echocardiography to detect the thickness of the ventricular septum in patients undergoing heart valve replacement surgery .The thickness of the ventricular septum over 11mm is defined as myocardial hypertrophy of patients, those less than or equal to 11mm were considered as non-hypertrophic controls. We collected a total of 6 cases of non-hypertrophic controls and 6 cases of myocardial hypertrophy patients' myocardial tissues, and Proteomic Analysis was performed by mass spectrometry.
2021-06-14 | PXD023778 | Pride