DOI: 10.5281/zenodo.8328679
title: A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration

description: Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" <strong>Structure</strong> <strong>ST_berghei_liver</strong> contains data generated during <em>stpipeline </em>analysis and imaging on 2k arrays Spatial Transcriptomics platform as well as data necessary for and from hepaquery analysis. These samples include 38 sections in total of which 8 are from mice (n=4) infected with sporozoites for 12h, 5 sections from control mice (n=3) at 12h, 7 sections from mice (n=4) infected with sporozoites for 24h and 4 sections from control mice (n=3) for 24 as well as 8 samples of mice (n=2) infected with sporozoites for 38h and control mice (n =2) for 38h. <strong><em>count</em></strong> contains gene expression matrix output from stpipeline in .tsv format <em><strong>spotfiles</strong> </em>contains coordinate files for count matrices <strong><em>images </em></strong>contains scaled H&E, Fluorescence (FL) and annotated H&E images (from FL annotations) scaled to 10% of the original image size. <em><strong>masks </strong></em>contains image masks for hepaquery analysis <strong><em>distances </em></strong>contains distance measurements from original section sorted by timepoint as well as combined across timepoints <strong>cluster</strong> contains clustering information across spatial positions used in spatial enrichment analysis <strong>STUtiility_mus_pb_ST.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>ST_berghei_liver</strong> <strong>visium_berghei_liver</strong> contains data generated with the <em>spaceranger </em>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include 8 sections in total, of which 1 was infected with sporozoites for 12h, 1 control section at 12h, 1 section infected with sporozoites for 24h and 1 control section at 24 as well as 2 sporozoite infected sections, and 2 control sections at 38h. <strong><em>V10S29-135_A1</em></strong> contains spaceranger output for section 1 for infected and control sections at 38h post-infection <em><strong>V10S29-135_B1</strong></em> contains spaceranger output for section 1 for infected and control sections at 12h post-infection <em><strong>V10S29-135_C1 </strong></em>contains spaceranger output for section 1 for infected and control sections at 24h post-infection <em><strong>V10S29-135_D1 </strong></em>contains spaceranger output for section 2 for infected and control sections at 38h post-infection <strong>se_visium.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>visium_berghei_liver</strong> <strong>snSeq_berghei_liver</strong> contains data generated with the <em>cellranger </em>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include single nuclei of 2 infected and control mice after 12h, 2 infected and control mice after 24h, 2 infected and control mice after 38h, and 2 uninfected mice prior to a challenge. <em><strong>cellranger_cnt_out</strong> </em>contains feature count matrix information from cell ranger output <strong>final_merged_curated_annotations_270623.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>snSeq_berghei_liver.tar.gz</strong> <strong>raw images.zip </strong>contains raw images for supplementary figures 20-22 <strong>adjusted images.zip </strong>contains brightness and contrast adjusted images for supplementary figures 20-22