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.
Project description:Purpose:The goal of this study was to evalute gene expression patterns of equine chorioallantoic membrane during different stages of the pregnancy Method: mRNA profile of equine chorioallantoic membrane (CAM) from 45days, 4months, 6months and 10months (4 samples for each time points) generated by RNA-sequencing,using a Illumina HiSeq 4000 ( HiSeq 4000 sequencing kit version 1). The sequence reads were trimmed for adapters and quality using TrimGalore Version 0.4.4,and then mapped to EquCab2.0 using STAR-2.5.2b. Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
