Published October 31, 2022 | Version 2022.10.31
Journal article Open

Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver

Authors/Creators

  • 1. Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, organLife Laboratory and D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
  • 2. Department of Internal Medicine V, Hematology and Oncology, and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
  • 3. Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
  • 4. Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
  • 5. Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Austria

Description

This archive contains input data, singularity containers as well as all results related to the single-cell RNA-seq analysis from the paper:

Hautz, Salcher, Fodor, et al. (2022). Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver

In particular, it contains the following files

  • input_data.zip: A h5ad file with unfiltered UMI counts
  • containers.zip: singularity containers with all software dependencies required to reproduce the analysis
  • results.zip: executed jupyter notebooks, plots and h5ad files with cell-type annotations. This archive can be computed based on the input data using the code published at: https://github.com/icbi-lab/nmp-liver

 

The raw data is available from GEO (GSE216584), but the processed data is enough to execute the analysis workflow.

Files

containers.zip

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