Development Core

Project Summary Breakthroughs in single-cell omics are providing unprecedented opportunities to investigate diverse biological questions including tissue heterogeneity, cell activity dynamics, fate determination and cellular responses to stress. Since first being described in 2009, single-cell technologies have developed rapidly, and currently most laboratories are performing single-cell RNA sequencing (scRNA-seq) using equipment from 10X Genomics based on droplet microfluidics. While powerful, this approach is expensive and relatively low throughput. An additional drawback to single cell technologies is that they lose spatial information due to tissue dissociation, so the physiological context cells in their niche is unknown. Understanding cellular gene expression in the context of tissue organization and morphology is critical to understanding cellular function and this is particularly true in chronic kidney disease (CKD) where injury, repair and fibrosis initiation occurs in the tubulointerstitial niche. The SCORE Core is a Resource Development Core that will address these limitations by developing and operationalizing cutting-edge technologies, and the computational pipelines required to interpret resulting data, to support the Biomedical Resource Cores and the broad kidney research community nationally. The aim of the SCORE Core is to develop new protocols and code that will illuminate the pathobiology of CKD, beginning with split pool barcoding based single nuclei multi-omics and high resolution in situ sequencing-based spatially resolved transcriptomics. We will develop protocols to employ simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq), a highly scalable approach for measurement of chromatin accessibility and gene expression in the same single cell, and the computational pipelines to analyze the resulting data. In addition, the SCORE Core will develop the protocols for high resolution in situ-sequencing based spatial transcriptomics using the Xenium platform. These protocols and code will be highly enabling to users in our Center, and to the Consortium broadly. The SCORE Core will also interact with the National O’Brien Consortium and Steering Committee to prioritize the development of future cutting edge technologies as they become available.