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Single-cell RNA sequencing elucidates cell populations in the murine and human tympanic membrane

ABSTRACT: Single-cell RNA sequencing elucidates cell populations in the murine and human tympanic membrane

PROVIDER: PRJNA529222 | ENA |

REPOSITORIES: ENA

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Single-cell RNA sequencing elucidates cell populations in the murine and human tympanic membrane

Project description:Previous descriptions of the cellular makeup of the tympanic membrane (TM) describe three basic cell types: keratinocytes, fibrofblasts, and muscosal cells. To better understand the diversity of cells in this tissue, we performed single-cell RNA sequencing on dissociated murine and human TMs. We identified the basic cell types previously known, as well as subtypes of cells in each group. Notably, keratinocyte cell clusters spanning the known differentiation kierarchy were identified, including two groups of undifferentiated keratinocytes which we propose make distinct contributions to maintaining the TM epidermis.

2020-11-03 | GSE128892 | GEO

Epimorphic Regeneration in the Mammalian Tympanic Membrane

Project description:Purpose: The goal of this study was to characterize the transcriptional response to injury of the murine tympanic membrane at multiple time points using single-cell RNA sequencing. Methods: mRNA profiles of Unwounded (Pars Tensa and Pars Flaccida) and Wounded (Day 1, Day 3, Day 7 and Day 14) murine tympanic membranes from WT FVB mice. The sequence reads that passed quality filters were analyzed at the transcript isoform level from fastq to matrix files using standard 10x genomics pipeline via CellRanger Results: Using the 10x Genomics Cell Ranger pipeline, we analyzed over 10,000 cells per timepoint from the UW and WO tympanic membranes, mapping the reads to the mouse genome (build mm10). The cells were then clustered primarily using the single-cell software package Seurat version 4. Conclusions: Our study represents the first detailed analysis of the regeneration timeline of the injured murine tympanic membrane, generated by RNA-seq technology. Our results show the emergence of novel populations on the tympanic membrane as it regenerates and characterizes the changes in all layers of the organ.

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Expression data of human tympanic membrane cells and epidermal keratinocytes [miRNA]

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Expression data of human tympanic membrane cells and epidermal keratinocytes [miRNA]

Project description:The data set compares the microRNA expression of two types of keratinocytes from the tympanic membrane and epidermis of the body. Healthy human samples were harvested for the analysis. Cells were cultivated to evaluate the effect of keratinocytes only. Few Chip Ids (11) were considered differentially expressed between the cell types. Six samples were analyzed in total. Each cell type in biological triplicates. Genes of p-value <0.05 and fold change of â¥ 1.5 were considered significant.

2016-05-31 | E-GEOD-76673 | biostudies-arrayexpress

Expression data of human tympanic membrane cells and epidermal keratinocytes [mRNA]

Project description:The data set compares the gene expression of two types of keratinocytes from the tympanic membrane and epidermis of the body. Healthy human samples were harvested for the analysis. Cells were cultivated to evaluate the effekt of keratinocytes only. 626 Chip Ids considered differentially expressed between the cell types. Enrichment tests show genes related to migration are over-represented in the highly expressed genes of TMK vs. EK.

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Expression data of human tympanic membrane cells and epidermal keratinocytes

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Microenvironment Cell Populations

Project description:Microenvironment Cell Populations

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RNA-seq of human adipose-derived mesenchymal stem cells cultured in hypoxia against normoxia controls, and human tympanic membrane keratinocytes

Project description:Human adipose-derived mesenchymal stem cells were cultured either in hypoxia (Hx; <0.1% oxygen) or standard culture conditions (normoxia, Nx) over 48 hours in serum-free medium. Human tympanic membrane keratinocytes were cultured in standard culture conditions over 48 hours in serum-free medium.

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The genetics of wound healing in tympanic membranes in rats

Project description:The aim of this study was to identify the genes differentially expressed between timepoints in the week following tympanic membrane perforation in rats. Tissue from 240 individual rats was used in this study following random allocation into timepoint groups to be sacrificed over 7 days. An Agilent one color microarray technique was performed and the results were analyzed using Genespring GX9 software. A total of 3262 genes were identified as significant (p<0.05) and differentially expressed above a two-fold threshold between the timepoints. This study provides a complete genetic review of rat tympanic membrane wound healing over 7 days. The results can be used as a model for other wound healing in other mammals and in different parts of the body. The information on differential gene expression can be used in research towards developing chronic tympanic membrane perforations and also in research to treat acute and chronic tympanic membrane perforations. The microarray was performed on animals in a disease free environment and the genetic information can be compared to future research in disease states of the TM including Otitis media, cholesteatoma, chronic perforation and tympanosclerosis.

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