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

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

PROVIDER: PRJEB42334 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5037650.fastq.gz	Fastqsanger.gz
	ERR5037660.fastq.gz	Fastqsanger.gz
	ERR5037670.fastq.gz	Fastqsanger.gz
	ERR5037680.fastq.gz	Fastqsanger.gz
	ERR5037690.fastq.gz	Fastqsanger.gz

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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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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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