DOI: 10.5281/zenodo.15359608
title: Spatiotemporal Transcriptomic Analysis of the Murine Kidney Reveals Compartment-Specific Changes During Cold Ischemic Injury

description: Kidney transplantation remains the gold standard treatment strategy for end-stage renal disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that may contribute to poor graft outcomes. However, the molecular characterization of potential mechanisms of cold ischemia injury remains incomplete. To bridge this knowledge gap, we leveraged spatial transcriptomics technology to perform full transcriptome characterization of cold ischemia injury (0-48 hours) using a murine model. We developed a computational workflow to identify spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a compartment-specific manner. We identified potential metabolic reprogramming preferentially within the kidney inner medulla displaying strong oxidative phosphorylation signature in an ischemic environment. We found commonalities between the spatiotemporal transcriptomic presentation of cold ischemia and warm ischemia‒reperfusion injury, including an induction of an anti-viral like immune response throughout the renal tissue. Altogether, these systems-level biological insights enabled by our full transcriptome temporal characterization unveil a molecular basis for how cold ischemia injury may negatively affect graft performance. Moreover, our spatial analyses highlight pathological developments deep within the renal tissue, suggesting potential opportunities for new insights beyond biopsy-focused superficial tissue examinations. 




Here, we provide processed spatial transcriptomics data, metadata, and relevant annotations derived through our computational workflow as described in the main article. 

 




There are four compressed folders corresponding to different durations of cold ischemia injury (CIS) i.e., 0, 12, 24 and 48 hours called:  








1_0hr.tar.gz 










2_12hr.tar.gz 










3_24hr.tar.gz  










4_48hr.tar.gz  





Each of these compressed folders contain folders called:  








spatial 










filtered_feature_bc_matrix 






These folders are standard outputs from the 10x Genomics SpaceRanger (v2.0.1) pipeline. 

 



1. The “spatial” subfolder folder contains the following files (descriptions from 10XGenomics):










Filename 









Description 











aligned_fiducials.jpg 









Aligned fiducials QC image 











aligned_tissue_image.jpg 









Aligned CytAssist and Microscope QC image. Present only for CytAssist workflow 











cytassist_image.tiff 









Input CytAssist image in original resolution that can be used to rerun the pipeline. Present only for CytAssist workflow 











detected_tissue_image.jpg 









Detected tissue QC image 











scalefactors_json.json 









Scale conversion factors for spot diameter and coordinates at various image resolutions 











spatial_enrichment.csv 









Downsampled full resolution image. The image dimensions depend on the input image and slide version. 











tissue_hires_image.png 









Downsampled full resolution image. The image dimensions depend on the input image and slide version. 











tissue_lowres_image.png 









Full resolution image downsampled to 600 pixels on the longest dimension. 











tissue_positions.csv 









csv file containing spot barcode, if the spot was called under (1) or out (0) of tissue; the array position, image pixel position x, and image pixel position y for the full resolution image. 









 

2. The “filtered_feature_bc_matrix” folder contains the following files: 










Filename 









Description 











barcodes.tsv.gz 









compressed file containing the barcode identity (16 nucleotide oligomer sequence) for each spot. 











features.tsv.gz 









compressed file containing gene names (features) along with their respective ensemble IDs. 











matrix.mtx.gz 









compressed sparse matrix file containing the raw gene counts information for each spot. 







Note: Count matrix (i.e., feature-barcode matrix) and position matrix can be constructed from these files using the code provided in the folder named 0.Count_&_Position_matrix_construction located within the following GitHub repository: https://github.com/ssingh95jhu/Cold_Ischemia_Injury_Molecular_Characterization.

 

3. The "structure_annotation.csv.gz" file contains spot barcode identity and their corresponding annotation belonging to one of the kidney compartments namely inner medulla, outer medulla, cortex and other. 

 

These files were used for a web application to interactively explore this data. Spot barcode identities have been modified to substitute ‘-’ with ‘.’ but are otherwise the same.