Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues: Supplementary Data
Description
Supplementary data for the study "Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues". The data.tar.gz archive contains: processed data files from 10x Visium experiments, immunofluorescence images and cell type proportion estimates generated with stereoscope. Scripts and rmarkdown files are available in the doc.tar.gz archive to run computational analyses related to the manuscript. data: 1 annotation/ - files used for gene symbol conversion 2 archivalcancer/ - spatially resolved transcriptomics data from FFPE archival soft tissue carcinoma (generated with spaceranger v1.0.0) 3 HGSC/ - spatially resolved transcriptomics data from FFPE High Grade Serous Carcinosarcoma, HGSC (generated with spaceranger v1.0.0) 4 immunofluorescence/ - raw images (TIF format) of immunostaining with a SARS-CoV-1 antibody and DAPI staining 5 kidneyorganoid/ - spatially resolved transcriptomics data from PFA fixed kidney organoids (generated with spaceranger v1.0.0) 6 lung_SARS-CoV-2/- spatially resolved transcriptomics data from FFPE lung tissue infected with SARS-CoV-2 (generated with spaceranger v1.0.0) 7 lungcellmarkers/ - table of DE genes from Lung cell atlas 8 lungorganoid/ - spatially resolved transcriptomics data from PFA fixed lung organoids (generated with spaceranger v1.0.0) 9 mousebrain/- spatially resolved transcriptomics data from FFPE mousebrain (generated with spaceranger v1.0.0) 10 registration/ - image registration related data objects generated with the wholebrain workflow 11 stereoscope/ - cell type proportions estimates through cell type mapping with stereoscope doc: 1 archival.Rmd - code for QC of archival samples 2 biotype_content_mouse_brain_data.Rmd - code for calculating and visualizing biotype content 3 fromHE_extended_FF.R - script to register FF coronal brain ection to the Allen Mouse Brain Atlas using the wholebrain workflow 4 fromHE_extended_FFPE.R - script to register FFPE coronal brain section to the Allen Mouse Brain Atlas using the wholebrain workflow 5 global_functions_segmentation.R - functions required for nuclei segmentation 6 global_functions.R - functions required for registration 7 HGSC.Rmd - analysis of FFPE High Grade Serous Carcinosarcoma (HGSC) tissue data 8 Kidney_organoids.Rmd - analysis of PFA Kidney organoids Visium data 9 Lung_organoids.Rmd - analysis of PFA Lung organoids Visium data 10 Lung_tissue_Covid19.Rmd - analysis of FFPE Lung tissue infected with Covid19 Visium data 11 mouse_brain_multiple_sections.Rmd - joint analysis of 7 FFPE mouse brain (coronal) tissue sections Visium data 12 mouse_FFPE_vs_FF.Rmd - comparison of Visium data obtained from FFPE and FF tissue (coronal mouse brain tissue sections) 13 QC_metrics_by_age.Rmd - analysis and visualization of QC over storage time 14 segmentation_of_SARS-Cov-1.Rmd - simple nuclei segmentation of DAPI stain images: High resolution Hematoxylin and Eosin stained bright field images in JPG format.