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 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. 

- 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