Work

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

Year: 2025

Type: article

Abstract: 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).

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.17409939

Authors: Uapinyoying, Prech, Jaiswal, Jyoti

Institutions: National Institutes of Health, Children's National, George Washington University

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

Funders: Silicon Valley Community Foundation, Eunice Kennedy Shriver National Institute of Child Health and Human Development