Development Core

项目摘要 单细胞组学的突破性进展为研究各种生物学提供了前所未有的机会。 问题包括组织异质性、细胞活性动力学、命运决定和细胞对 应力自2009年首次描述以来，单细胞技术发展迅速，目前大多数 实验室正在使用10 X Genomics的设备进行单细胞RNA测序（scRNA-seq） 基于液滴微流体技术。虽然功能强大，但这种方法昂贵且吞吐量相对较低。一个 单细胞技术的另一个缺点是它们由于组织解离而丢失了空间信息， 所以在它们的小生境中的生理背景细胞是未知的。了解细胞基因表达在 组织组织和形态的背景对于理解细胞功能至关重要， 在慢性肾脏疾病（CKD）中尤其如此，其中损伤、修复和纤维化起始发生在肾脏中。 小管间质龛SCORE核心是解决这些限制的资源开发核心 通过开发和实施尖端技术，以及所需的计算管道， 解释结果数据，以支持生物医学资源核心和广泛的肾脏研究社区 全国范围内。SCORE核心的目标是开发新的协议和代码， CKD的病理生物学，开始于基于单核多组学和高分辨率的分裂池条形码， 基于原位测序的空间分辨转录组学。我们将制定协议， 高通量ATAC和RNA表达测序（SHARE-seq），一种高度可扩展的方法， 在同一单个细胞中测量染色质可及性和基因表达，以及计算 管道来分析结果数据。此外，SCORE核心将开发用于高 基于分辨率原位测序的空间转录组学，使用Xenium平台。这些协议和 代码将为我们中心的用户以及广泛的联盟提供高度支持。SCORE核心还将 与国家奥布莱恩联盟和指导委员会互动，优先发展未来 尖端技术的应用。

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.