Cited by 1,422Single-cell and spatial transcriptomicsGenomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

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Rosenberg, Alexander B., Roco, Charles M., Muscat, Richard A., Kuchina, Anna, Sample, Paul, Yao, Zizhen, Graybuck, Lucas T., Peeler, David J. +6 more·2018·Science

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Abstract

To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path toward comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.

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  • A method using four rounds of combinatorial barcoding uniquely labelled over 100,000 nuclei in one experiment.

    “method, uniquely labelled over 100,000 nuclei in one experiment using four rounds of combinatorial barcoding58”
  • SPLiT-seq, a plate-based RNA method, gave unique labels to more than 100,000 nuclei in a single run through four rounds of combinatorial barcoding.

    “Split-pool ligation-based transcriptome sequencing (SPLiT-seq), a plate-based transcriptomics method, uniquely labelled over 100,000 nuclei in one experiment using four rounds of combinatorial barcoding58.”
  • hSpS cluster annotation overall matched previously annotated mouse spinal cord clusters.

    “We found that, overall, cluster annotation in hSpS matched previously annotated spinal cord clusters”

    From Generation of Functional Human 3D Cortico-Motor Assembloids (2020) · cites this paper as Rosenberg et al., 2018

  • The merged dataset contains over one hundred thousand cells and nuclei from the first six published studies of the postnatal mouse spinal cord.

    “We first created a merged dataset with over one hundred thousand cells and nuclei from the first six published studies of the postnatal mouse spinal cord1–6.”
  • The general feature of lower robustness in mid and ventral clusters is consistent with previous observations and likely reflects similar patterns of gene expression amongst mid and ventral clusters.

    “This general feature was consistent with previous observations and likely reflects similar patterns of gene expression amongst mid and ventral clusters1,4.”

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Authors
Rosenberg, A. B., Roco, C. M., Muscat, R. A., Kuchina, A., Sample, P., Yao, Z., Graybuck, L. T., Peeler, D. J., Mukherjee, S., Chen, W., Pun, S. H., Sellers, D. L., Tasic, B., & Seelig, G.
Affiliations
  • University of Washington (US)
  • Allen Institute for Brain Science (US)
Corresponding author
  • Rosenberg, Alexander B.
  • Roco, Charles M.
  • Seelig, Georg
Venue
Science
Published
2018-04-13
Volume
360
Issue
6385
Pages
176-182
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W2794083495
Cited by
1,422
References
98
Citations by year
2026: 112 · 2025: 172 · 2024: 248 · 2023: 161 · 2022: 154 · 2021: 189 · 2020: 177 · 2019: 127 · 2018: 70 · 2017: 11
FWCI
51.05
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Science Foundation (CCF-1317653)
  • National Institutes of Health (TL1 TR002318)
  • National Institute of General Medical Sciences (R01CA207029)
  • National Institute of Neurological Disorders and Stroke (R01NS064404, R21NS086500)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
single-cell RNA sequencing, combinatorial barcoding, single-nucleus transcriptomics, mouse brain development, spinal cord development, postnatal development, central nervous system, cell type annotation, developmental lineage, pseudotime, sample multiplexing
MeSH terms
Animals, Brain, Cell Nucleus, Humans, Neurons, Spinal Cord, Sequence Analysis, RNA, Gene Expression Regulation, Developmental, Gene Expression Profiling, NIH 3T3 Cells, Mice, HEK293 Cells, Single-Cell Analysis, Transcriptome

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