Parabiosis single-cell data viewer
Project Status
Complete
Project Deliverables
Posit Connect interface that enables interactive exploration of the data
Project Description
The Rubin lab studies aging using heterochronic parabiosis, a surgical procedure whereby young and old mice are joined together so that they share a common circulatory system. To better understand aging-associated brain deterioration and potentially modifiable or even reversible aspects of it, the Rubin lab has performed single-cell transcriptomic profiling of young and old mouse brains after parabiosis. The data consists of 10x Genomics single-cell RNA-seq measurements for roughly 160k cells obtained from heterochronic pairs in which 3- to 4-month-old mice were joined with 20- to 22-month-old mice. In a collaboration with HMS Research Computing, CCB equipped the Rubin lab with a cloud-based Posit Connect server, and helped deploying a performant R/Shiny application to the server to enable interactive exploration of the data.
Outcomes
Parabiosis data viewer: https://rubinlab.connect.hms.harvard.edu/parabiosis/
Publications
This project contributed to the research for the publications listed below:
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Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types
Authors: Methodios Ximerakis, Kristina M. Holton, Richard M. Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M. Shah, Jill M. Goldstein, Caterina Gasperini, Ioannis A. Gampierakis, Scott L. Lipnick, Sean K. Simmons, Sean M. Buchanan, Amy J. Wagers, Aviv Regev, Joshua Z. Levin & Lee L. Rubin
Nature Aging ,09 March 2023