Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:Metagenome sequencing All specimens were collected and immediately stored in a -80 freezer. All BALF samples were subjected to MS. DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech). DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China). Bioinformatic pipeline analysis Low-quality and short (<35 bp) reads were removed from raw data using fastp [10]. Remaining reads were mapped to the human reference genome (hg19) using the Burrows-Wheeler method to remove sequences of human origin. Filtered reads were classified with RefSeq, downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/).
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.
