sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons
The Sox family of transcription factors plays a crucial role in the development of the vertebrate nervous system. In the zebrafish embryo, sox1 genes are expressed in neural progenitor cells and neurons of the ventral spinal cord. We recently reported that the loss of function of sox1a and sox1b results in a significant decrease in a subtype of V2 neurons, called V2s, in zebrafish. Here a single-cell RNA sequencing (scRNA-Seq) approach was used to analyse the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four different time points during the development of an earlier established Tg(sox1a:EGFP) line. In addition to the sox1a-expressing neurons described previously, we found that this gene is also expressed in late-developing intraspinal serotonin neurons (ISNs). Developmental trajectory analysis of single-cell data and morpholino knockdown of lateral floor plate (LFP) cells expressing the nkx2.9 gene suggest that ISNs are generated from LFP progenitor cells. Pharmacological inhibition of the Notch signalling pathway demonstrates the necessity of this pathway for the development of LFP progenitor cells into ISN populations. Our results confirm that the zebrafish LFP is a progenitor domain from which ISN neurons are generated in addition to the previously described KA" and V3. Overall design: The trunk and tail of Tg(sox1a:eGFP) lines were and dissected at 1, 2 3 and 5 dpf. The tissue  was dissociated and GFP positive cells were sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation, cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom (GRChZ 11) and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit, and Sequencing done by Illumina.