Single-Cell Transcriptomics

Through collaborations with multiple laboratories, biotechnology companies, and the National Institutes of Health, we have been part of a team of scientists working towards uncovering the mysteries of the human brain through the analysis of **single-cell transcriptomes**.

Our group was one of the first to sequence DNA and RNA from human brain cells. Importantly, these Jackson Pollock-like transcriptomic displays, which reflect enormous single-cell transcriptome diversity in the brain, are entirely consistent with the existence of underlying somatic genomic mosaicism (GM), e.g., (Lee at al., Nature 2018).

Key Articles

RNA isoform diversity in human neurodegenerative diseases

Liu CS, Park C, Ngo T, Saikumar J, Palmer CR, Shahnaee A, Romanow WJ, Chun J. eNeuro. 2024

Single-Nucleus RNA-seq of Normal-Appearing Brain Regions in Relapsing-Remitting vs. Secondary Progressive Multiple Sclerosis: Implications for the Efficacy of Fingolimod

Kihara Y, Zhu Y, Jonnalagadda D, Romanow W, Palmer C, Siddoway B, Rivera R, Dutta R, Trapp BD, Chun J.. Frontiers in Cellular Neuroscience. 2022.

Altered cell and RNA isoform diversity in aging Down syndrome brains

Palmer CR, Liu CS, Romanow WJ, Lee MH, Chun J. PNAS 2021.

Characterizing Transcriptional Heterogeneity Through Pathway and Gene Set Overdispersion Analysis

Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV. Nat Methods 2016;13(3):241-244.

Neuronal Subtypes and Diversity Revealed By Single-Nucleus RNA Sequencing of the Human Brain

Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung H-L, Chen S, Vijayaraghavan R, Wong J, Chen C, Sheng X, Kaper F, Shen R, Ronaghi M, Fan J-B, *Wang W, *Chun J, *Zhang K. Science 2016;352(6293):1586-1590.
*co-senior authors

A Comparative Strategy for Single-Nucleus and Single-Cell Transcriptomes Confirms Accuracy in Predicted Cell-Type Expression From Nuclear RNA

Lake BB, Codeluppi S, Yung YC, Chun J, Kharchenko PV, Linnarsson S, Zhang K. Sci Rep 2017;7(1):6031.

Integrative Single-Cell Analysis of Transcriptional and Epigenetic States in the Human Adult Brain

Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K. Nat Biotechnol 2018;36(1):70-80.