PUBLICATION
Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq
- Authors
- Pandey, S., Shekhar, K., Regev, A., Schier, A.F.
- ID
- ZDB-PUB-180327-9
- Date
- 2018
- Source
- Current biology : CB 28(7): 1052-1065.e7 (Journal)
- Registered Authors
- Schier, Alexander
- Keywords
- adult, habenula, in situ atlas, larva, neuronal types, single-cell RNA-seq, transcriptomes, zebrafish
- Datasets
- GEO:GSE109158, GEO:GSE109159, GEO:GSE105115
- MeSH Terms
-
- Animals
- Gene Expression Regulation, Developmental*
- Habenula/anatomy & histology*
- Habenula/growth & development
- Habenula/metabolism
- High-Throughput Nucleotide Sequencing/methods*
- Larva
- Neurogenesis
- Neurons/cytology*
- Neurons/metabolism
- Single-Cell Analysis/methods*
- Zebrafish/genetics*
- Zebrafish/growth & development
- Zebrafish/physiology
- Zebrafish Proteins/genetics*
- PubMed
- 29576475 Full text @ Curr. Biol.
Citation
Pandey, S., Shekhar, K., Regev, A., Schier, A.F. (2018) Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq. Current biology : CB. 28(7):1052-1065.e7.
Abstract
The identification of cell types and marker genes is critical for dissecting neural development and function, but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single-cell RNA-seq (scRNA-seq) with anatomical brain registration to create a comprehensive map of the zebrafish habenula, a conserved forebrain hub involved in pain processing and learning. Single-cell transcriptomes of ∼13,000 habenular cells with 4× cellular coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a reference atlas created a resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly, despite brain growth and functional maturation, cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping