Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1021940 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26222520_1.fastq.gz | Fastqsanger.gz | |||
| SRR26222520_2.fastq.gz | Fastqsanger.gz | |||
| SRR26222521_1.fastq.gz | Fastqsanger.gz | |||
| SRR26222521_2.fastq.gz | Fastqsanger.gz | |||
| SRR26222522_1.fastq.gz | Fastqsanger.gz |
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Project description:Background The skin maintains the body’s integrity and serves as the first line of defence against pathogens, stressors and mechanical injuries. Despite the global significance of salmon in aquaculture, how cells transcriptomic profile varies during wound healing, remains unexplored. Teleost contain adult pluripotent cells that differentiate into various tissues, including bone, cartilage, tendon, ligament, adipose, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism´s lifespan and actively participate in the wound healing processes. In this study, we characterise the transcriptomic profiles of putative mesenchymal stromal cells (fibroblast-like adult stem cells) in healthy Atlantic salmon tissue and during the wound healing process. Results Single-nucleus sequencing and spatial transcriptomics were used to detect transcriptomic changes occurring during wound healing that are commonly associated with mesenchymal stromal cells. We followed the transcriptomic activity of these cells during an in vivo wound healing time course study showing that these cells become more transcriptionally active during the remodelling stage of wound healing. The changes detected give insights into the potential differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. Conclusions We chart the transcriptomic activity of sub-clusters of putative differentiating stromal cells during the process of wound healing for the first time, revealing different spatial niches of the various putative MSC subclusters, and setting the stage for further investigation of the manipulation of transitioning cell types to improve fish health. KEYWORDS: Salmo salar, skin, mesenchymal stromal cells, single-cell sequencing, spatial transcriptomics, wound healing, spatial niche.
2025-01-15 | GSE287051 | GEO
Project description:This study aimed to explore the therapeutic potential of cyano-phycocyanin (C-PC) to improve the efficiency of chronic refractory wound healing processes. The hormone induced chronic refractory skin ulcer model were established on the backs of mice. Assessment of wound-healing efficiency of C-PC was evaluated by analyzing total wound closure, recovery percentage and epidermal thickness of wounds. Hematoxylin-eosin, Masson trichrome and immunohistochemical analysis were performed to evaluate the re-epithelialization, inflammatory response, granulation tissue formation and fibrotic tissue formation. Differentially expressed genes were identified through RNA-seq, polymerase chain reaction (PCR) array and confirmed by quantitative PCR (qPCR). Cell viability was determined using a cell counting kit-8 (CCK-8) assay, migration and angiogenesis were detected by wound healing and tube formation assays. The related protein expression was analyzed by Western blot. The results demonstrated a significantly higher wound-healing rate in C-PC group compared to the control group at 3, 7, 14, and 21 days (p< 0.05). The mechanism may involve increased collagen accumulation, promotion of angiogenesis and reduction in the infiltration of inflammatory cells. Additionally, VEGFR-2 was highly likely to be the target for C-PC. Thus, C-PC may hold potential for the treatment of wound healing and ischemic/ reperfusion injuries.
2025-06-01 | GSE296266 | GEO
Project description:The mechanism of cardiomyocyte prliferation and migration after ventricular resection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying post-injury heart regeneration and wound healing progress via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks to provide insights into the ventricular resection wound healing mechanism.
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Project description:Wound priming in epidermal Lrig1 stem cell progeny leads to a more efficient response to future injuries. To understand if primed progenitors maintain during aging the transcriptional program acquired during wound healing in young age, we performed single cell RNA-Seq of Lrig1 stem cell progeny 40 weeks after injury.
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Project description:Corneal injuries remain a major cause of consultation in the ophthalmology clinics worldwide. Repair of corneal wounds is a complex mechanism that involves cell death, migration, proliferation, differentiation, and extracellular matrix (ECM) remodeling. In the present study, we used a tissue-engineered, two-layers (epithelium and stroma) human cornea as a biomaterial to study both the cellular and molecular mechanisms of wound healing. Gene profiling on microarrays revealed important alterations in the pattern of genes expressed by tissue-engineered corneas in response to wound healing. Expression of many MMPs-encoding genes was shown by microarray and qPCR analyses to increase in the migrating epithelium of wounded corneas. Many of these enzymes were converted into their enzymatically active form as wound closure proceeded. In addition, expression of MMPs by human corneal epithelial cells (HCECs) was affected both by the stromal fibroblasts and the collagen-enriched ECM they produce. Most of all, results from mass spectrometry analyses provided evidence that a fully stratified epithelium is required for proper synthesis and organization of the ECM on which the epithelial cells adhere. In conclusion, and because of the many characteristics it shares with the native cornea, this human two layers corneal substitute may prove particularly useful to decipher the mechanistic details of corneal wound healing. Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 7), Collagen type I (number of replicates: 2), Collagen type IV (number of replicates: 2), Fibronectin (number of replicates: 2), Tenascin C (number of replicates: 2) and Laminin (number of replicates: 2) matrix. Central, internal and external ring of wounded Tissue-engineered human cornea.
2015-11-25 | E-GEOD-75336 | biostudies-arrayexpress
Project description:Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the main events participating in the healing of a wound, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process, but allow exploring many unanswered features of the healing response; e.g., which are the signal(s) responsible for initiating tissue remodeling? How is the sealing of the epithelia achieved? Or which are the inhibitory cues that cancel the healing machinery upon completion? Answering these and other questions demands in first place the identification and functional analysis of wound-specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method to culture imaginal discs that allows live imaging and biochemical analysis and is healing-permissive. Employing this approach, we performed a comparative genome-wide profiling between those Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. This lets us identify a set of potential wound-specific genes. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in a healing assay. This non-saturated analysis defines a relevant set of new genes whose changes in expression levels are functionally significant for proper tissue repair. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound response. We developed a healing-permissive in vitro culture system for fly imaginal discs: we used one-channel microarrays for comparing healing-engaged cells (showing activation of the JNK signaling cascade) to cells not participating in healing (silent JNK activity) in wounded wing imaginal discs in culture. Employing this method, we aimed detecting the relevant genes involved in disc healing through microarray analysis. We compared cells actively involved in healing to those not involved and identified a whole set of upregulated or downregulated genes. They were annotated, clustered by expression profiles, chromosomal locations and presumptive functions. Most importantly, we functionally tested them genetically in a healing assay.
2015-04-13 | E-GEOD-62863 | biostudies-arrayexpress