Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease

This dataset contains raw and processed seqFISH data quantifying 1300 genes within single cells from three Acute Kidney Injury (AKI) and three control mice kidneys. The dataset also contains the codebook and probe sequences used to create probe libraries for the seqFISH experiments.

Supplementary_data_tables folder contains the supplementary data tables for the manuscript: Data_1 contains DE gene expression, Data_2 and Data_3 contain the codebook and probe sequence information needed to generate the probe libraries used for the seqFISH experiments. Data_4 contains the probe sequence information needed to generate the serial probes against Vcam1 and Havcr1

AKI_Ctrl_object.rds - Seurat object generated from seqFISH data for the AKI and healthy control mice as detailed in the manuscript.

Counts_raw.csv contains raw gene counts for all cells in the dataset.

coordinates.csv contains the xy coordinates (in um) for every cell in the dataset.

metadata.csv contains the metadata for each cell in the dataset including sample and cell type allocation as well as Microenvironment (ME) assignment. This file also contains expression data of Vcam1 and Havcr1, which were detected using serial probes as detailed in the manuscript.