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Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons
Open accessAbstract
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.
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“Recent advances in single-nucleus RNA sequencing (snRNA-Seq) have extended transcriptomic analysis to frozen or archived post-mortem brain tissues.”
From Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions (2025) · cites this paper as [165]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“This technique has enabled detailed profiling of vulnerable neuronal subtypes and glial populations.”
From Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions (2025) · cites this paper as [165]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“By isolating nuclei rather than whole cells, snRNA-Seq retains transcriptional fidelity while avoiding cell dissociation artifacts155,165.”
From Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions (2025) · cites this paper as [165]
In the citing paper
“However, these methods either rely on sorting nuclei by FACS into plates (96 or 384 wells)3,5 or on C1 microfluidics4, neither of which are scalable, precluding profiling tens of thousands of nuclei”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“the DroNc-seq sub-clusters matched with a nearly one-to-one mapping to sub-clusters defined by sNuc-Seq3 on the hippocampus, and with a satisfactory match to sets of fine-resolution sub-clusters defined by scRNA-seq of a distinct brain region, the visual cortex17”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“we found good congruence between our GABAergic sub-clusters and those previously defined3,4,17 in mouse and human”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“reflecting the enrichment of nascent transcripts in the nucleus3,13–16”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“the cell types and their signatures from DroNc-seq are comparable to those obtained previously with sNuc-Seq of mouse hippocampus3 and scRNA-seq of the visual cortex17”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“The cell-type specific gene signatures we determined for each human cell-type cluster (Fig. 2d, Supplementary Table 8) agreed well with previously defined signatures in mouse hippocampus3 and cortex17”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“To address this challenge, we3 and others4–6 developed single nucleus RNA-seq (snRNA-seq) for analysis of RNA in single nuclei from fresh, frozen or lightly fixed tissues.”
From Massively parallel single-nucleus RNA-seq with DroNc-seq (2017) · cites this paper as [3]
In the citing paper
“Differentiation trajectories of newborn neurons and oligodendrocytes in adults can also be reconstructed (Habib et al., 2016; Marques et al., 2016).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Habib et al., 2016
In the citing paper
“Continuous trajectories occur during brain development (Nowakowski et al., 2017) and in differentiating cell populations in the adult, such as oligodendrocyte lineage cells (Marques et al., 2016) or newborn granule cells in the dentate gyrus of the hippocampus (Habib et al., 2016).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Habib et al., 2016
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Metadata
- Authors
- Habib, N., Li, Y., Heidenreich, M., Swiech, L., Avraham-Davidi, I., Trombetta, J. J., Hession, C., Zhang, F., & Regev, A.
- Affiliations
- Broad Institute (US)
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
- Corresponding author
- Habib, Naomi
- Li, Yinqing
- Zhang, Feng
- Regev, Aviv
- Venue
- Science
- Published
- 2016-08-26
- Volume
- 353
- Issue
- 6302
- Pages
- 925-928
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC5480621
- OpenAlex
- W2486882743
- Cited by
- 601
- References
- 63
- Citations by year
- 2026: 30 · 2025: 51 · 2024: 71 · 2023: 59 · 2022: 63 · 2021: 75 · 2020: 67 · 2019: 58 · 2018: 73 · 2017: 46 · 2016: 7
- FWCI
- 31.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- Howard Hughes Medical Institute
- Helen Hay Whitney Foundation
- Human Frontier Science Program
- Klarman Cell Observatory at the Broad Institute
- National Institute of Mental Health (U01MH105960)
- NIMH (5DP1-MH100706, 1R01-MH110049)
- NSF
- New York Stem Cell
- Simons
- Paul G. Allen Family
- Vallee Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single-nucleus RNA sequencing, adult neurogenesis, newborn neurons, cell proliferation, transcriptional dynamics, rare cell types
- MeSH terms
- Animals, Cell Division, Cell Nucleus, Deoxyuridine, Hippocampus, Isotope Labeling, Neurons, Spinal Cord, Transcription, Genetic, Sequence Analysis, RNA, Mice, Neurogenesis, Single-Cell Analysis, Transcriptome
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