github link
Accession IconSRP129440

Smart-seq2 analysis of larval zebrafish habenula from the gng8-GFP transgenic line

Organism Icon Danio rerio
Sample Icon 1138 Downloadable Samples
Technology Badge IconNextSeq 500

Submitter Supplied Information

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 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 ~13000 habenular cells (>4x coverage) identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich 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. Overall design: gng8-GFP zebrafish heads were dissected, dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart-seq2. A total of 22 gng8-GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart-seq2.
PubMed ID
Total Samples
Submitter’s Institution
No associated institution
Alternate Accession IDs


Show of 0 Total Samples
Accession Code
Specimen part
Processing Information
Additional Metadata
No rows found