DOI: 10.5061/dryad.bnzs7h4hj
title: Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease

description: Kidney injury disrupts the intricate renal architecture and triggers
 limited regeneration, and injury-invoked inflammation and fibrosis.
 Deciphering molecular pathways and cellular interactions driving these
 processes is challenging due to the complex renal architecture. Here, we
 apply single cell spatial transcriptomics to examine ischemia-reperfusion
 injury in the mouse kidney. Spatial transcriptomics reveals
 injury-specific and spatially-dependent gene expression patterns in
 distinct cellular microenvironments within the kidney and predicts
 Clcf1-Crfl1 in a molecular interplay between persistently injured proximal
 tubule cells and neighboring fibroblasts. Immune cell types play a
 critical role in organ repair. Spatial analysis reveals cellular
 microenvironments resembling early tertiary lymphoid structures and
 identifies associated molecular pathways. Collectively, this study
 supports a focus on molecular interactions in cellular microenvironments
 to enhance understanding of injury, repair and disease.
description: # Spatial transcriptomics defines injury-specific microenvironments in the
 adult mouse kidney and novel cellular interactions in regeneration and
 disease
 [https://doi.org/10.5061/dryad.bnzs7h4hj](https://doi.org/10.5061/dryad.bnzs7h4hj) This dataset contains processed RDS object used to generate the figures in the manuscript as well as the metadata, raw gene counts and cell locations in csv format. ## **Description of the data and file structure:** '**AKI_Ctrl_object.rds'** : This file contains the .Rds object which has been processed by Suerat as described in the manuscript. * ‘CellID’: Unique identifier for each cell in the dataset ordered as [sampleID]_[Position in Sample]_cell_[numerical ID] * ‘orig.ident’: Original ID for each sample * 'SampleID': Identifier of each samle (3 control mice and 3 mice which undewent IRI treatment as detailed in the manuscript) * ‘nCount_Spatial’: Total number of RNA transcripts detected in each cell for the Spatial assay * 'nFeature_Spatial': Total number of unique genes detected in each cell for the Spatial assay * 'Group': column specifying which group the cell belongs to – either Ctrl (control mouse) or IRI treatment (AKI mouse). * ‘Celltype’ : column specifying the cell type allocation of each cell * ‘area’: area of the cell mask in pixel units * ‘eccentricity’: eccentricity value of each cell mask. Eccentricity of 0 is a perfect circle, eccentricity values between 0 and 1 represent an ellipse with values closer to 1 represent elongation of the cell mask. * ‘log10_Vcam1.antibody’: log normalized values of Vcam1 antibody staining for each cell. NA values appear in samples where Vcam1 antibody was not used. * ‘T_annot’ : column specifying the cell type allocation with subdivision of T cells into CD4, Treg, CD8_naive, CD8_eff_mem (effector memory) and CD8_exhusted. * ‘ME’: Microenvironment cluster allocation for each cell.   * ‘Vcam1_raw’: raw counts for Vcam1 serial RNA probe. NA values appear in one sample (IRI1) where Vcam1 was not measured. * ‘Vcam1_Norm’: normalized values of Vcam1_raw. Values were normalized the same way as the barcoded genes in the dataset. * ‘Havcr1_raw’: raw counts for HAvcr1 serial RNA probe. NA values appear in one sample (IRI) where Havcr1 was not measured. * ‘Havcr1_Norm’: normalized values of Havcr1_raw. Values were normalized the same way as the barcoded genes in the dataset. **'metadata.csv'** : Metadata for the RDS object. The columns are the same as detailed above. **'coordinates_raw.csv'** : This file contains the xy coordinates of the cells in micrometers. * 'CellID': Unique identifier for each cell in the dataset as in the RDS and metadata files. * 'SampleID': Sample identifier as in the RDS and metadata files. * 'x_um': X location of each cell in micrometers. * 'y_um': Y location of each cell in micrometers. **'Counts_raw.csv'** : This file contains raw gene counts matrix. The first column is the cell ID which corresponds to the CellID in metadata, coordinates and RDS object. the second column is the sampleID corresponding to the other csv files and the RDS object. The following columns are the expression values of the seqFISH genes.