Fluorescence images of ybx1 mutant neuromasts [time course, wt]

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 tha..., 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 Tg(atoh1a:dTomato) 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)., , # Fluorescence images of ybx1 mutant neuromasts [time course, wt]

[https://doi.org/10.5061/dryad.g1jwstr1z](https://doi.org/10.5061/dryad.g1jwstr1z)

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...,

与人类内耳的感觉器官类似，斑马鱼（Danio rerio）等鱼类的侧线神经丘（neuromasts, NMs）中含有机械感觉毛细胞（hair cells, HCs），其周围被称为支持细胞的祖细胞所包裹。受损的神经丘可通过在祖细胞中表达毛细胞特异性基因（如调控毛细胞命运的主调控因子atoh1a），快速再生出新的毛细胞。我们采用监督学习算法DELAY，推断了再生过程中神经丘的早期基因调控网络（gene-regulatory network, GRN），并鉴定出可促进斑马鱼幼鱼侧线毛细胞快速再生的适应性机制。该网络的核心枢纽为Y盒结合蛋白1（Y-box binding protein 1, ybx1），其在毛细胞祖细胞与新生毛细胞中高表达，且能够识别鲤科鱼类atoh1a候选再生响应启动子元件中的DNA结合基序。我们发现，来自ybx1突变型斑马鱼幼鱼的神经丘在毛细胞数量上存在稳定的、再生特异性缺陷，且毛细胞再生与atoh1a基因表达的启动速度均比……慢20%。
为标记毛细胞，我们将3~5日龄（days post fertilization, dpf）的斑马鱼躯干用含0.1%吐温-20的4%甲醛磷酸缓冲盐溶液（0.1% PBST）固定：可在室温下固定1小时，或于4℃条件下固定过夜。对于Tg(atoh1a:dTomato)转基因幼鱼，我们先用0.5% PBST清洗斑马鱼躯干，随后在含1%牛血清白蛋白（bovine serum albumin, BSA）的0.05% PBST封闭液中于室温孵育1小时；再更换含DAPI（1:200）、鬼笔环肽（phalloidin, 1:40）及山羊抗tdTomato DyLight550偶联抗体（1:50；美国圣地亚哥MyBioSource公司）的新鲜封闭液孵育2小时。最后用1×PBS再次清洗躯干20~30分钟，随后封片并使用搭载微透镜超分辨率成像系统（VT-iSIM，英国VisiTech International公司）的奥林巴斯IX83倒置共聚焦显微镜以100倍物镜进行成像。
# ybx1突变型神经丘荧光图像 [时间进程组，野生型]
https://doi.org/10.5061/dryad.g1jwstr1z

本研究共包含4个数据集，具体如下：
* ybx1突变型神经丘荧光图像 [自交组]（DOI: 10.5061/dryad.v15dv4257）：包含发育与再生过程中野生型、杂合突变型及纯合突变型幼鱼的神经丘图像
* ybx1突变型神经丘荧光图像 [时间进程组，野生型]（DOI: 10.5061/dryad.g1jwstr1z）：野生型幼鱼固定神经丘的时间进程图像
* ybx1突变型神经丘荧光图像 [时间进程组，杂合型]（DOI: 10.5061/dryad.jh9w0vtn5）：杂合突变型幼鱼固定神经丘的时间进程图像
* ybx1突变型神经丘荧光图像 [Ybx1免疫荧光组]（DOI: 10.5061/dryad.wm37pvn0h）：野生型与杂合突变型幼鱼神经丘的免疫染色图像

数据与文件结构说明
本数据集包含荧光……