DOI: 10.5061/dryad.v15dv4257
title: Fluorescence images of ybx1 mutant neuromasts [incross]

description: Like the sensory organs of the human inner ear, the lateral-line
 neuromasts (NMs) of fish such as the zebrafish (Danio rerio) contain
 mechanosensory hair cells (HCs) that are surrounded by progenitors called
 supporting cells. Damaged NMs can quickly regenerate new HCs by expressing
 in the progenitors HC-specific genes such as atoh1a, the master regulator
 of HC fate. We used the supervised learning algorithm DELAY to infer
 regenerating NMs’ early gene-regulatory network (GRN) and identify
 adaptations that promote the rapid regeneration of lateral-line HCs in
 larval zebrafish. The central hub in the network, Y-box binding protein 1
 (ybx1), is highly expressed in HC progenitors and young HCs and can
 recognize DNA-binding motifs in cyprinids’ candidate
 regeneration-responsive promoter elements for atoh1a. We showed that NMs
 from ybx1 mutant zebrafish larvae display consistent,
 regeneration-specific deficits in HC number and initiate both HC
 regeneration and atoh1a expression 20 % slower than in siblings. By
 demonstrating that ybx1 promotes rapid HC regeneration through early
 atoh1a upregulation, the results support DELAY’s ability to identify key
 temporal regulators of gene expression.
description: To label HCs, we fixed 3-5 dpf zebrafish trunks with 4%
 formaldehyde in phosphate-buffered saline (PBS) solution with 0.1 %
 Tween-20 (0.1 % PBST) for either 1 hr at room temperature or overnight at
 4 °C. For inbred <em>ybx1</em> mutant offspring, we washed
 trunks for 30 m in fresh 0.1 % PBST, followed by a 1 hr incubation at room
 temperature in 0.05 % PBST with DAPI (1:200) and Alexa Fluor Plus 405
 phalloidin (1:40; Invitrogen, Eugene, USA). We washed trunks once more for
 20-30 m in 1X PBS before mounting and imaging at 100X on an Olympus IX83
 inverted confocal microscope with a microlens-based super-resolution
 imaging system (VT-iSIM, VisiTech International).
description: # Fluorescence images of ybx1 mutant neuromasts [incross]
 [https://doi.org/10.5061/dryad.v15dv4257](https://doi.org/10.5061/dryad.v15dv4257) This study is comprised of four datasets as follows: * Fluorescence images of ybx1 mutant neuromasts [incross] (DOI: 10.5061/dryad.v15dv4257): Neuromasts from wild-type, heterozygous, and homozygous mutant larvae during development and regeneration * Fluorescence images of ybx1 mutant neuromasts [time course, wt] (DOI: 10.5061/dryad.g1jwstr1z): Time-course images of fixed neuromasts from wild-type larvae * Fluorescence images of ybx1 mutant neuromasts [time course, het] (DOI: 10.5061/dryad.jh9w0vtn5): Time-course images of fixed neuromasts from heterozygous mutant larvae * Fluorescence images of ybx1 mutant neuromasts [Ybx1 immunofluorescence] (DOI: 10.5061/dryad.wm37pvn0h): Immunostaining images in neuromasts from wild-type and heterozygous mutant larvae ## Description of the data and file structure This data set contains fluorescence images of fixed neuromasts from inbred *ybx1* mutant zebrafish larvae. Each image comprises: 1) an `nd` file with parameters, *e.g.*, X/Y resolution; and, 2) a single-channel fluorescence image (excitation = 405 nm; emission = 460 nm), showing nuclear DAPI and apical phalloidin signals. ### Files and variables #### File: ybx1_mutant.tar **Description:** Main directory with sub-directories for each genotype and condition * Sub-directories are labeled by development (`dev`) or regeneration (`regen`) and genotype (wild-type [`wt`], heterozygous [`het`], or homozygous mutant [`mut`]) - Files are labeled with numerical identifiers for unique larvae (`zf`) and neuromast (`nm`), generally arranged from anterior to posterior per-larva - Imaging parameters: &gt; Exposure = 500 ms &gt; *IllumSetting* = iSIM \_405_460 &gt; *MagNA* = 1.35 &gt; *MagRI* = 1.406 &gt; *MagSetting* = 100X SiOil &gt; wavelength = 460 &gt; Width: 95.128 microns (2068) &gt; Height: 65.504 microns (1424) &gt; Depth: 25.2000 microns (126) &gt; Resolution: 21.7391 pixels per micron &gt; Voxel size: 0.046x0.046x0.2 micron^3