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README.md

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Description

This is the repository for the scripts used in the study "Immune infiltration is associated with distinct transcriptional states and metabolic profiles in chordomas", iScience (2026), https://doi.org/10.1016/j.isci.2026.115668.

This repository has the following structure:

  1. input_files - .txt & .RData files containing the necessary input to perform the analysis e.g. annotation files and processed data files.
  2. GeoMx - scripts used for analyzing the GeoMx DSP data & generating the figures - also includes the imaging mass cytometry figure.
  3. MALDI - scripts used for analyzing the MALDI-MSI data & generating the figures.
  4. Other - scripts used for analyzing the other data & generating the figures - PAS/dPAS, IHC & qPCR.

Authors

S. van Oost, R. Ursem, Z.B. Erdem, S. Cardoso, S. Venneker, R. van der Breggen, I.H. Briaire-de Bruijn, A.B. Kruisselbrink, W.C. Peul, K. Szuhai, R.J.P van der Wal, R. van Zeijl, B. Heijs, N.F.C.C. de Miranda & J.V.M.G. Bovee

Data availability

  1. GeoMx DSP (raw and processed): https://figshare.com/s/4d52d0129b9e0f9c7a8c
  2. MALDI-MSI (raw): https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000100742
  3. MALDI-MSI (processed): upon request | https://figshare.com/s/4d52d0129b9e0f9c7a8c
  4. Imaging mass cytometry data (raw): https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD830?query=S-BIAD830
  5. Imaging mass cytometry data (processed): https://github.com/deMirandaLab/multimodal-profiling-of-chordomas