Spatial transcriptomics datasets for "Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumours and breast cancer"

Spatial transcriptomics datasets for "Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumours and breast cancer" This repository contains KB1P mouse mammary tumour and human breast cancer 10x Visium datasets generated and analysed in our article: Demeter Túrós, Morgane Decollogny, Astrid Chanfon, Myriam Siffert, Lou Romanens, Jean-Christophe Tille, Olivier Tredan, Intidhar Labidi-Galy, Alberto Valdeolivas, and Sven Rottenberg."Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumours and breast cancer." GitHub: https://github.com/rottenberglab/residual-disease Archive Contents The databases folder contains input files for functional analysis. The qupath_annotations folder holds a QuPath project file with pathologist annotations, which are used to transfer annotations to capture spots. The visium_mouse and visium_human folders contain 10x Visium datasets for mouse mammary tumors and human breast cancer, respectively. Each dataset folder includes metadata CSV files. Additionally, cell type deconvolution results for the mouse dataset (inferred cell type abundances), and the transferred annotations for both, are stored as CSV files within these folders. Within both the visium_mouse and visium_human folders, you will also find: An enrichment_scores folder containing CSV files with gene set enrichment and scoring analysis results. A space_ranger_outputs folder storing Space Ranger output files for each sample. A processed folder containing AnnData objects in .h5ad format (details below). Details 1. mouse_main contains the main dataset of 25 mouse mammary tumour samples as well as 2 control samples. Tumour samples: '20220401-1_1', '20220401-1_2', '20220401-1_3', '20220401-2_6', '20220401-2_7', '20220401-2_8', '20221010-1_1', '20221010-1_2', '20221010-1_3', '20221010-1_4', '20221010-2_5', '20221010-2_6', '20221010-2_7', '20221010-2_8', '20221010-3_10', '20221010-3_11', '20221010-3_12', '20221010-3_9', '20221010-4_13', '20221010-4_14', '20221010-4_15', '20221010-4_16', '20230607-1_1', '20230607-2_5', '20230607-2_8'. Healthy controls: '20220401-1_4', '20220401-2_5'. AnnDatas contain the following metadata:var: 'spatially_variable_sample' (classified as spatially variable in the sample), 'morans_i' (Moran's I value), 'spatially_variable_dataset' (classified as spatially variable in the whole dataset).obsm: 'adaptive_mutability' (gene set score for adaptive mutability), 'cell2loc' (cell type deconvolution abundances inferred with cell2location), 'cell_cycle_activity' (gene set score for cell cycle genes), 'chr_aa' (tissue compartment scores identified with Chrysalis), 'copy_number_variation' (copy number variation data calculated with infercnvpy),'hallmarks_of_cancer' (gene set scores for hallmarks of cancer), 'msigdb_hallmarks' (gene set scores for MSigDB hallmarks), 'progeny_pathway_activity' (pathway activity scores calculated with PROGENy), 'sasp' (gene set score for senescence-associated secretory phenotype). 2. mouse_imc contains the IMC dataset of 7 mouse mammary tumour samples. Samples: '20230607-1_2', '20230607-1_3', '20230607-1_4', '20230607-2_5', '20230607-2_6', '20230607-2_7', '20230607-2_8'. Among these, '20230607-2_5' and '20230607-2_8' primary tumour samples were also analysed in the main dataset. Samples '20230607-1_3', '20230607-2_5', '20230607-2_6', and '20230607-2_8' were subjects of the analysis presented in the article, whereas all samples are presented in the supplementary information. AnnDatas contain the following metadata:var: 'morans_i' (Moran's I value), 'spatially_variable' (classified as spatially variable).obsm: 'cell2loc' (cell type deconvolution abundances inferred with cell2location), 'cell_cycle_activity' (gene set score for cell cycle genes), 'chr_aa' (tissue compartment scores identified with Chrysalis), 'hallmarks_of_cancer' (gene set scores for hallmarks of cancer), 'imc_cell_abundance' (cell type abundances mapped from the IMC data), 'imc_intensity' (mean intensity of IMC channels measured within cell segmentation masks falling within capture spots), 'progeny_pathway_activity' (pathway activity scores calculated with PROGENy), 'pt_content' (total Pt content of cells mapped from the IMC data), 'sasp' (gene set score for senescence-associated secretory phenotype). 3. visium_human contains 5 human breast cancer samples. Please refer to the IMPORTANT_README.txt when loading the human samples from the space_ranger_outputs folder. AnnDatas contain the following metadata:obs: 'annotations' (pathologist annotations), 'emt_signature' (EMT signature score), 'proliferating_signature' (proliferation signature score).var: 'spatially_variable' (classified as spatially variable in the whole dataset), 'morans_i' (Moran's I value).obsm: 'chr_aa' (tissue compartment scores identified with Chrysalis).