Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
IF: 63.714
Cited by: 2,393


The mammalian cerebral cortex supports cognitive functions such as sensorimotor integration, memory, and social behaviors. Normal brain function relies on a diverse set of differentiated cell types, including neurons, glia, and vasculature. Here, we have used large-scale single-cell RNA sequencing (RNA-seq) to classify cells in the mouse somatosensory cortex and hippocampal CA1 region. We found 47 molecularly distinct subclasses, comprising all known major cell types in the cortex. We identified numerous marker genes, which allowed alignment with known cell types, morphology, and location. We found a layer I interneuron expressing Pax6 and a distinct postmitotic oligodendrocyte subclass marked by Itpr2. Across the diversity of cortical cell types, transcription factors formed a complex, layered regulatory code, suggesting a mechanism for the maintenance of adult cell type identity.


Gene Expression

MeSH terms

CA1 Region, Hippocampal
Eye Proteins
Gene Expression
Genetic Markers
Homeodomain Proteins
Inositol 1,4,5-Trisphosphate Receptors
PAX6 Transcription Factor
Paired Box Transcription Factors
Repressor Proteins
Sequence Analysis, RNA
Single-Cell Analysis
Somatosensory Cortex
Transcription Factors


Zeisel, Amit
Muñoz-Manchado, Ana B
Codeluppi, Simone
Lönnerberg, Peter
La Manno, Gioele
Juréus, Anna
Marques, Sueli
Munguba, Hermany
He, Liqun
Betsholtz, Christer
Rolny, Charlotte
Castelo-Branco, Gonçalo
Hjerling-Leffler, Jens
Linnarsson, Sten

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