title: Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
abstract: 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.
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Amit
authors.initials: A
authors.lastname: Zeisel
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Ana B
authors.initials: AB
authors.lastname: Muñoz-Manchado
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Simone
authors.initials: S
authors.lastname: Codeluppi
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Peter
authors.initials: P
authors.lastname: Lönnerberg
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Gioele
authors.initials: G
authors.lastname: La Manno
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Juréus
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Sueli
authors.initials: S
authors.lastname: Marques
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Hermany
authors.initials: H
authors.lastname: Munguba
authors.affiliation: Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, S-751 85 Uppsala, Sweden.
authors.forename: Liqun
authors.initials: L
authors.lastname: He
authors.affiliation: Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, S-751 85 Uppsala, Sweden. Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Christer
authors.initials: C
authors.lastname: Betsholtz
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Rolny
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Gonçalo
authors.initials: G
authors.lastname: Castelo-Branco
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden. sten.linnarsson@ki.se jens.hjerling-leffler@ki.se.
authors.forename: Jens
authors.initials: J
authors.lastname: Hjerling-Leffler
authors.affiliation: Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden. sten.linnarsson@ki.se jens.hjerling-leffler@ki.se.
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
mesh_terms: D000818:Animals; D056547:CA1 Region, Hippocampal / Q000166:cytology* / Q000378:metabolism; D005136:Eye Proteins / Q000235:genetics; D015870:Gene Expression; D005819:Genetic Markers; D018398:Homeodomain Proteins / Q000235:genetics; D053496:Inositol 1,4,5-Trisphosphate Receptors / Q000235:genetics; D007395:Interneurons / Q000145:classification* / Q000166:cytology / Q000378:metabolism; D051379:Mice; D009836:Oligodendroglia / Q000145:classification* / Q000166:cytology / Q000378:metabolism; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics; D010802:Phylogeny; D012097:Repressor Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013003:Somatosensory Cortex / Q000166:cytology* / Q000378:metabolism; D014157:Transcription Factors / Q000145:classification / Q000235:genetics; D059467:Transcriptome
chemical_list: D005136:Eye Proteins; D005819:Genetic Markers; D018398:Homeodomain Proteins; D053496:Inositol 1,4,5-Trisphosphate Receptors; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; C000605732:Pax6 protein, mouse; D012097:Repressor Proteins; D014157:Transcription Factors