Fig. 1: Experimental design.
From: Multimodal spatial transcriptomic characterization of mouse kidney injury and repair
A Mouse kidney samples were collected at various time points (hour 4, hour 12, day 2, day 14, and week 6) after bilateral ischemia-reperfusion injury (BIRI). N = 1 mice per group. The measurement of blood urea nitrogen (BUN) levels confirmed the acute injury to the kidneys. Kidneys were preserved as formalin-fixed, paraffin-embedded (FFPE) tissue blocks. Serial sections of 6 μm thickness obtained from FFPE blocks were mounted onto slides for spatial transcriptomics analysis. The experimental workflow comprises three main steps: (1) Xenium in situ profiling with a customized 300-gene panel was performed on one section, followed by post-Xenium Periodic Acid Schiff (PAS) staining. (2) An adjacent section was stained with hematoxylin and eosin (H&E) and transferred to the Visium CytAssist platform for whole-transcriptome profiling. (3) A shared coordinate system was established for aligning morphology images and molecular data from both platforms. Morphology images were aligned to their respective cell/spot point data. (Created in BioRender. Humphreys, B. (https://BioRender.com/blvpfyn). B Representative post-Xenium PAS staining images across IRI time points. Scale bar: 40 μm. C Quantified tubular lesion scores. D Representative Sirius Red staining images. Scale bar: 40 μm. E Quantified interstitial fibrosis scores.
