Description

This is the repository for the scripts used in the study "Multimodal profiling of chordoma immunity reveals distinct immune contextures", J Immunother Cancer (2024), http://dx.doi.org/10.1136/jitc-2023-008138

This repository has the following structure:

1. input_files - .tsv files containing the necessary input to perform the analysis e.g. annotation files and processed data files.
2. RNAseq - scripts used for analysing the RNA sequencing data & generating the figures. See GEO link below for raw data of chordomas.
3. IMC - scripts used for analysing the imaging mass cytometry data & generating the figures. See BioImage Archive link for raw data.
4. IF - scripts used for analysing the multispectral immunofluorescence & generating the figures. Also includes the cox proportional hazard analysis.
5. TCRseq_HLA - scripts used for analysing the TCR sequencing data & generating the figures. Also includes the HLA class I-related figures.

Authors

S. van Oost, D.M. Meijer, M.E. IJsselsteijn, J. Roelands, B. van den Akker, R. van der Breggen, I.H. Briaire-de Bruijn, M. van der Ploeg, P.M. Wijers-Koster, S.B. Polak, W.C. Peul, R.J.P. van der Wal, N.F.C.C. de Miranda & J.V.M.G. Bovee

Data availability

RNAseq data (GEO): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239531 Imaging mass cytometry data (BioImage): https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD830?query=S-BIAD830