DOI: 10.5061/dryad.jh9w0vtn5
title: Fluorescence images of ybx1 mutant neuromasts [time course, het]

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 <em>Tg(atoh1a:dTomato)</em> larvae, we washed trunks
 in 0.5 % PBST and incubated them for 1 hr at room temperature in 0.05 %
 PBST blocking solution with 1 % BSA and again for 2 hr in fresh blocking
 solution with DAPI (1:200), phalloidin (1:40) and goat anti-tdTomato
 DyLight550-conjugated antibodies (1:50; MyBioSource, San Diego, 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 [time course, het]
 [https://doi.org/10.5061/dryad.jh9w0vtn5](https://doi.org/10.5061/dryad.jh9w0vtn5) 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 outcrossed *ybx1* mutant and *Tg(atoh1a:dTomato)* zebrafish larvae. Each image comprises: 1) an `nd` file with parameters, *e.g.*, X/Y resolution; and, 2) two-channel fluorescence images, showing DAPI and phalloidin (405/460 nm) and dTomato (561/600 nm) signals. ### Files and variables #### File: ybx1_het_x_atoh1a_dtom_het.tar **Description:** Main directory with sub-directories for each time point * Sub-directories are labeled by time points at `12`, `16`, `20`, and `24` hours post-ablation * Files are labeled with numerical identifiers for unique larvae (`zf`) and neuromast (`nm`), as well as excitation/emission wavelengths * Imaging parameters: &gt; Exposure = 500 ms &gt; *WaveName1* = “iSIM_405*460*” &gt; *WaveName2* = “*iSIM_561_600/50*” &gt; *_MagNA* = 1.35 &gt; *MagRI* = 1.406 &gt; *MagSetting* = 100X SiOil &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