Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses

This repository contains the results related to the spatial RNA-seq analysis performed for the publication: "Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses", except for the raw (.fastq) data which will be depositied on the NCBI: SRA database. The larger integrated Seurat objects (.rds), and RCTD reference objects (.rds) are placed in the root folder. The rest of the files have been grouped into human and mouse visium zip files. Files in the zip are organized following the folder structure outlined in the analysis code/notebooks used to generate these results which are archived on Zenodo (https://doi.org/10.5281/zenodo.17455196). The most up to date version of the code can be found on github (https://github.com/Ped-SkM-Cell-Atlas/SkM_preservation_manuscript) Other files included are SpaceRanger output files such as the matrix files (.mtx, .h5), H&E images (.tif), loupe alignment files (.json) which can also be found on GEO. In addition to the downstream GSEA output, plots (.pdf), and exported calculations (.csv).