title: Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.
abstract: 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.
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA 02142, USA. McGovern Institute of Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Naomi
authors.initials: N
authors.lastname: Habib
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA 02142, USA. McGovern Institute of Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Yinqing
authors.initials: Y
authors.lastname: Li
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA 02142, USA. McGovern Institute of Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Matthias
authors.initials: M
authors.lastname: Heidenreich
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA 02142, USA. McGovern Institute of Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Swiech
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
authors.forename: Inbal
authors.initials: I
authors.lastname: Avraham-Davidi
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: Trombetta
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Hession
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Stanley Center for Psychiatric Research, 75 Ames Street, Cambridge, MA 02142, USA. McGovern Institute of Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. zhang@broadinstitute.org aregev@broadinstitute.org.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. zhang@broadinstitute.org aregev@broadinstitute.org.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D002455:Cell Division / Q000235:genetics; D002467:Cell Nucleus / Q000378:metabolism*; D003857:Deoxyuridine / Q000031:analogs & derivatives / Q000032:analysis; D006624:Hippocampus / Q000166:cytology / Q000378:metabolism; D007553:Isotope Labeling; D051379:Mice; D055495:Neurogenesis / Q000235:genetics*; D009474:Neurons / Q000166:cytology* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013116:Spinal Cord / Q000378:metabolism / Q000473:pathology; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: C031086:5-ethynyl-2'-deoxyuridine; D003857:Deoxyuridine