Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics: datasets

You can find here the datasets used in the publication: "Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics"
Alberto Valdeolivas, Bettina Amberg, Nicolas Giroud, Marion Richardson, Eric J.C. Gálvez, Solveig Badillo, Alice Julien-Laferrière, Demeter Turos, Lena Voith von Voithenberg, Isabelle Wells, Amy A. Lo, Emilio Yángüez, Meghna Das Thakur, Michael Bscheider, Marc Sultan, Nadine Kumpesa, Björn Jacobsen, Tobias Bergauer, Julio Saez-Rodriguez, Sven Rottenberg, Petra C. Schwalie, Kerstin Hahn
bioRxiv, 2023; doi: https://doi.org/10.1101/2023.01.23.525135 This contents the raw Spatial Transcriptomics data, spot categorization made by pathologist, the results of the deconvolution and intermediary files required to run the analysis described in our manuscript and available in Github: https://github.com/alberto-valdeolivas/ST_CRC_CMS In particular, you will find here several zip compressed files with the following content: - Intermediary_FileObjects.zip: The intermediary files generated in the scripts hosted in the github repo and required to run some later scripts. - IntermediaryFiles_ST_CRC_LiverMetastasis.zip: The intermediary files generated in the scripts hosted in the github repo and required to run some of the scripts dealing with the external CRC ST dataset used in our manuscript. - Pathology_SpotAnnotations.zip: The categories assigned by the pathologists to all the spots across our set ST samples to a different anatomical category (tumor, stroma, non-neoplastic mucosa...) - SN048_A121573_Rep1.zip, SN048_A121573_Rep2.zip, SN048_A416371_Rep1.zip, SN048_A416371_Rep2.zip, SN123_A551763_Rep1.zip, SN123_A595688_Rep1.zip, SN123_A798015_Rep1.zip, SN123_A938797_Rep1_X.zip, SN124_A551763_Rep2.zip, SN124_A595688_Rep2.zip, SN124_A798015_Rep2.zip, SN124_A938797_Rep2.zip, SN84_A120838_Rep1.zip, SN84_A120838_Rep2.zip: The output of Space Ranger, including processed count data matrices and histological images, for the ST data generated in this study - DeconvolutionResults_ST_CRC_BelgianCohort.zip, DeconvolutionResults_ST_CRC_KoreanCohort.zip, DeconvolutionResults_ST_CRC_LiverMetastasis.zip: These files contain the main results obtained when using the Cell2Location deconvolution approach in our samples (with two different references: Korean and Belgian cohorts) and in the external set of CRC ST samples (only Korean cohort)