Single-cell RNA sequencing (RNA-Seq) provides rich information about cell types and states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation of rare neurons from adult tissue is challenging and markers for each phase are limited. Here, we develop Div-Seq, which combines scalable single-nucleus RNA-Seq (sNuc-Seq) with pulse labeling of proliferating cells by 5-ethynyl-2′-deoxyuridine (EdU) to profile individual dividing cells. sNuc-Seq and Div-Seq can sensitively identify closely related hippocampal cell types and track transcriptional dynamics of newborn neurons within the adult hippocampal neurogenic niche, respectively. We also apply Div-Seq to identify and profile rare newborn neurons in the adult spinal cord, a noncanonical neurogenic region. sNuc-Seq and Div-Seq open the way for unbiased analysis of diverse complex tissues.
Bibliographical noteFunding Information:
Raw data are deposited to the Gene Expression Omnibus with accession no. GSE84371; annotated data are available at https://portals.broadinstitute.org/single-cell, and software tools are available at https://github.com/yinqingl/nucseq-analysis. We thank N. Friedman, A. Shalek, D. Gennert, T. Blosser, S. Kadosch, O. Rosen, Z. Wang, P. Rogers, and L. Gaffeny for support and J. Campbell for dissociated neurons image. N.H. is a Howard Hughes Medical Institute Fellow of the Helen Hay Whitney Foundation. M.H. is supported by the Human Frontier Science Program. This work was supported by the Klarman Cell Observatory at the Broad Institute and National Institute of Mental Health (NIMH) grant U01MH105960 (F.Z., A.R.). F.Z. is supported by the NIH through NIMH (5DP1-MH100706 and 1R01-MH110049), NSF, the New York Stem Cell, Simons, Paul G. Allen Family, and Vallee Foundations; and James and Patricia Poitras, Robert Metcalfe, and David Cheng. A.R. is a Howard Hughes Medical Institute Investigator on the scientific advisory board of Syros Pharmaceuticals and Thermo Fisher and a consultant for Driver group. N.H., Y.L., A.R., and F.Z. are inventors on provisional patent application 62/311,129, applied for by the Broad Institute and MIT, that covers the methods described in this paper. All DNA constructs are available from Addgene subject to a material transfer agreement with Addgene.