GeoMx DSP and MALDI-MSI data

Raw counts and Q3 normalized log2 counts from NanoString's GeoMx Digital Spatial Profiler, for 14 chordoma resection specimens. ROIs were segmented into tumor and stroma and interrogated with the Whole Transcriptome Atlas (WTA) from NanoString.Includes .RData files with the NanoStringObjects and separate .csv files with the counts and metadata..RData filles can be read as RDS into R.Metadata from the MALDI-mass spectrometry imaging data, including the UMAP and clusters, for 16 chordoma resection specimens from 13 patients. Spots were clustered and subsequently classified as tumor or stroma by aligning cluster spatial localization with the corresponding H&E image for each specimen.Includes a .csv file with the UMAP and clustering metadataRaw data or processed peak matrices can be shared upon request.R scripts used to process the data are available on our group's GitLab at https://git.lumc.nl/bstp/papers/spatial-profiling-of-chordomas.