Welcome to the repository for "ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts" by Caleb C. Reagor, Paloma Bravo & A. J. Hudspeth (2025).

Datasets contains the pre-processed scRNA-seq data from baek2022_preprocessing.R to fine-tune DELAY and infer the early GRN for neuromast regeneration in hair cells (HC) and central supporting cells (SC).

zfish-tfs-baek2022.csv contains a list of known TFs in the data set.

Figure 1

DELAY_GRN_analysis.py contains code for the analyses of the inferred GRN for early neuromast regeneration.

enhancer_regions.R extracts locations of genes' enhancers for de novo inference of Ybx1's TFBS with MEME Suite (see fimo.tsv & streme.txt).

Figure 2

Microscopy contains quantifications and code for the analyses of ybx1 mutant neuromasts and Ybx1 immunostaining.