Journal Article

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

Kuchina, Anna, Graybuck, Lucas T., Sellers, Drew L., Roco, Charles M., Peeler, David J., Seelig, Georg, Sample, Paul, Muscat, Richard A., Chen, Wei, Mukherjee, Sumit, Yao, Zizhen, Tasic, Bosiljka, Rosenberg, Alexander B., Pun, Suzie H.

2018

Overview

The recent development of single-cell genomic techniques allows us to profile gene expression at the single-cell level easily, although many of these methods have limited throughput. Rosenberg et al. describe a strategy called split-pool ligation-based transcriptome sequencing, or SPLiT-seq, which uses combinatorial barcoding to profile single-cell transcriptomes without requiring the physical isolation of each cell. The authors used their method to profile >100,000 single-cell transcriptomes from mouse brains and spinal cords at 2 and 11 days after birth. Comparisons with in situ hybridization data on RNA expression from Allen Institute atlases linked these transcriptomes with spatial mapping, from which developmental lineages could be identified. Science , this issue p. 176 Single-cell analyses with SPLiT-seq (split-pool ligation-based transcriptome sequencing) elucidate development of the mouse nervous system. 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.

• Publisher: The American Association for the Advancement of Science
• Subject: Anatomy / Animals / Brain / Brain - growth & development / Cell Nucleus - genetics / Central nervous system / Combinatorial analysis / Gene expression / Gene Expression Profiling - methods / Gene Expression Regulation, Developmental / Gene mapping / Gene sequencing / HEK293 Cells / Humans / Individualized Instruction / Mice / Multiplexing / Neurons - metabolism / NIH 3T3 Cells / Nuclei (cytology) / Ribonucleic acid / RNA / Rodents / Sequence Analysis, RNA / Single-Cell Analysis - methods / Spinal cord / Spinal Cord - growth & development / Transcription / Transcriptome