DOI: 10.5061/dryad.fqz612k3s
title: Data for: Atoh1 is required for the formation of lateral line electroreceptors and hair cells, whereas Foxg1 represses an electrosensory fate

description: In electroreceptive jawed fishes and amphibians, individual lateral line
 placodes form lines of neuromasts on the head containing mechanosensory
 hair cells, flanked by fields of ampullary organs containing
 electroreceptors - modified hair cells that respond to weak electric
 fields. Extensively shared gene expression between neuromasts and
 ampullary organs suggests that conserved molecular mechanisms are involved
 in their development, but a few transcription factor genes are restricted
 either to the developing electrosensory or mechanosensory lateral line.
 Here, we used CRISPR/Cas9-mediated mutagenesis in G0-injected sterlet
 embryos (Acipenser ruthenus, a sturgeon) to test the function of three
 such genes. We found that the 'hair cell' transcription factor
 gene Atoh1 is required for both hair cell and electroreceptor
 differentiation in sterlet, and for Pou4f3 and Gfi1 expression in both
 neuromasts and ampullary organs. These data support the conservation of
 developmental mechanisms between hair cells and electroreceptors.
 Targeting ampullary organ-restricted Neurod4 did not yield any phenotype,
 potentially owing to redundancy with other Neurod genes that we found to
 be expressed in sterlet ampullary organs. After targeting
 mechanosensory-restricted Foxg1, ampullary organs formed within neuromast
 lines, suggesting that Foxg1 normally represses their development, whether
 directly or indirectly. We speculate that electrosensory organs may be the
 'default' fate of lateral line primordia in electroreceptive
 vertebrates.
description: # Data for: Atoh1 is required for the formation of lateral line
 electroreceptors and hair cells, whereas Foxg1 represses an electrosensory
 fate Dataset DOI: [10.5061/dryad.fqz612k3s](10.5061/dryad.fqz612k3s) ##
 Description of the data and file structure In this dataset you will find
 images of sterlet sturgeon (*Acipenser ruthenus*) larvae underlying the
 data reported in **Supplementary Table 1** of the preprint Minařík M,
 Campbell AS, Franěk R, Vazačová M, Havelka M, Gela D, Pšenička M, Baker
 CVH (2024) *bioRxiv* 2023.04.15.537030 (DOI: 10.1101/2023.04.15.537030)
 and **Supplementary File 1**, **Supplementary File 2** and **Supplementary
 File 3** of the paper Minařík M, Campbell AS, Franěk R, Vazačová M,
 Havelka M, Gela D, Pšenička M, Baker CVH (2025) *eLife TBC* The dataset
 contains four main folders (zip archives): **Supplementary_File_1_Tyr**
 corresponds to the *Tyr* crispant data in Supplementary Table 1 of the
 preprint and Supplementary File 1 of the paper (Breakdown by sgRNA mix of
 CRISPR/Cas9 experiments). *Note:* Most of the *Tyr* crispant data are
 shared between this study and Campbell et al. (2025, DOI:
 [https://doi.org/10.7554/eLife.99798](https://doi.org/10.7554/eLife.99798)). **Supplementary_Files_1-2_Atoh1** corresponds to the *Atoh1* crispant data in Supplementary Table 1 of the preprint, Supplementary File 1 of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments) and Supplementary File 2 of the paper (Breakdown by individual crispant of *Atoh1* crispant phenotypes). **Supplementary_File_1_Neurod4** corresponds to the *Neurod4* crispant data in Supplementary Table 1 of the preprint and Supplementary File 1 of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments). **Supplementary_Files_1-3_Foxg1** corresponds to the *Foxg1* crispant data in Supplementary Table 1 of the preprint, Supplementary File 1 of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments) and Supplementary File 3 of the paper (Breakdown by individual crispant of *Foxg1* crispant phenotypes). Images are of sterlet sturgeon larvae after chromogenic *in situ* hybridization (ISH) and in some cases after post-ISH immunostaining for Sox2. Images were focus-stacked using HeliconFocus software (HeliconSoft). Individual focus slices are not included here. For phenotype assessment and publication, the brightness and contrast of some images were adjusted, but these further changes were not applied to the image files presented here. All methods are fully described in the Materials and Methods section of the associated publication. ### Files and variables #### File: Supplementary\_File\_1\_Tyr.zip **Description:** Images in this folder (zip archive) underlie the *tyrosinase* (*Tyr*) crispant data reported in Supplementary Table 1 of the preprint and **Supplementary File 1** of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments). *Note*: Most of the *Tyr* crispant data are shared between this study and Campbell et al. (2025, DOI: [https://doi.org/10.7554/eLife.99798](https://doi.org/10.7554/eLife.99798)).  Image files are organised into **Melanin** and **Other_markers** subfolders (matching the organisation of Supplementary File 1 of the paper). In the **Melanin** subfolder, images are further organised into subfolders based on the sgRNA mix used; each sgRNA-mix subfolder includes a "no_phenotype" subfolder for images of *Tyr* crispants without a phenotype (i.e., no effect on melanin pigmentation). Images of melanin pigmentation were not taken for 31 non-phenotypic Tyr crispants from Supplementary File 1 of the paper (all 24 analysed larvae for *Tyr* sgRNA 5+6, and 9 out of 15 non-phenotypic larvae for *Tyr* sgRNA 7+8). In the **Other_markers** subfolder, images are further organised into subfolders based on the sgRNA mix used and the ISH marker analysed (*Cacna1d*, *Gfi1*, *Kcnab3* or *Pou4f3*). *Filenames in Supplementary_File_1_Tyr:* Filenames include the CRISPR/Cas9 target gene (Tyr), sgRNA mix (sgRxxx) and a unique 2-digit or 3-digit code (see section "Abbreviations in filenames" below). Filenames include, where relevant, the ISH marker used (Cacna1d or Kcnab3) and "a-Sox2" if post-ISH immunostaining was performed with the anti-Sox2 antibody. Filenames end in a 6-digit date in yy.mm.dd format, with or without periods (e.g., 21.03.08 or 211020). This corresponds to the date the ISH protocol was started or, for images of melanin pigmentation, the date of the imaging. *Abbreviations in filenames:* Ar, *Acipenser ruthenus*; Ar45, *Acipenser ruthenus* stage 45; sgRxxx_yyy_, sgRNA mix plus 3-digit crispant code (e.g., sgR12_097\_ corresponds to sgRNA mix 1+2, crispant 97); sgRxx_NPyy_, sgRNA mix plus 2-digit code for non-phenotypic crispant (e.g., sgR14_NP03\_ corresponds to sgRNA mix 1+4, non-phenotypic crispant 3); sgRxx_YPyy_, sgRNA mix plus 2-digit code for phenotypic crispant (e.g., sgR14_YP19\_ corresponds to sgRNA mix 1+4, phenotypic crispant 19); wmD, wholemount dorsal view; wmL, wholemount left-side lateral view; wmR, wholemount right-side lateral view; wmV, wholemount ventral view. #### File: Supplementary\_Files\_1-2\_Atoh1.zip **Description:** **Description:** Images in this folder (zip archive) underlie the *Atoh1* crispant data reported in Supplementary Table 1 of the preprint, **Supplementary File 1** of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments) and **Supplementary File 2** of the paper (Breakdown by individual crispant of *Atoh1* crispant phenotypes). Image files are contained in a subfolder indicating the sgRNA mix used (sgRNA 1+2 for all *Atoh1* crispants) and further organised into subfolders based on the ISH marker analysed (*Cacna1d, Gfi1, Kcnab3* or *Pou4f3*). Within each subfolder, images of *Atoh1* crispants without a phenotype are included in a separate "no_phenotype" subfolder, where relevant. This matches the organisation of Supplementary File 2 of the paper. *Note:* Non-phenotypic *Atoh1* crispant 51, analysed with *Cacna1d* (batch 9), was recorded as "no phenotype" but not imaged. *Filenames in Supplementary_Files_1-2_Atoh1* Filenames include the CRISPR/Cas9 target gene (Atoh1), sgRNA mix (sgR12) and a unique 3-digit code (see section "Abbreviations in filenames" below). Filenames include the ISH marker used (Cacna1d, Gfi1, Kcnab3 or Pou4f3) and end in a 6-digit date in yymmdd format (e.g., 211020). This corresponds to the date the ISH protocol was started. *Note: Atoh1* crispants 49 and 50 were analysed with a paddlefish (*Polyodon spathula*) riboprobe against *Cacna1d*, indicated in the relevant filenames as PsCacna1d. *Abbreviations in filenames:* Ar, *Acipenser ruthenus*; Ar45, *Acipenser ruthenus* stage 45; Ps, *Polyodon spathula* riboprobe; sgR12_yyy_, sgRNA 1+2 mix plus 3-digit crispant code (e.g., sgR12_104\_ corresponds to sgRNA mix 1+2, crispant 104); wmD, wholemount dorsal view; wmL, wholemount left-side lateral view; wmR, wholemount right-side lateral view; wmV, wholemount ventral view. #### File: Supplementary\_File\_1\_Neurod4.zip **Description:**  Images in this folder (zip archive) underlie the *Neurod4* crispant data reported in Supplementary Table 1 of the preprint and **Supplementary File 1** of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments). Image files are organised into subfolders based on the sgRNA mix used and the ISH marker analysed (*Cacna1d or* Kcnab3). Within each subfolder, all images are included in a separate "no_phenotype" subfolder, as no phenotypes were observed for any *Neurod4* crispants. *Filenames in Supplementary_File_1_Neurod4* Filenames include the CRISPR/Cas9 target gene (Neurod4), sgRNA mix (sgRxxx) and a unique 3-digit code (see section "Abbreviations in filenames" below). Filenames include, where relevant, the ISH marker used (Cacna1d or Kcnab3) and end in a 6-digit date in yymmdd format (e.g., 211020). This corresponds to the date the ISH protocol was started. *Abbreviations in filenames:* Ar, *Acipenser ruthenus*; Ar45, *Acipenser ruthenus* stage 45; sgRxxx_yyy_, sgRNA mix plus 3-digit crispant code (e.g., sgR3456_058\_ corresponds to sgRNA mix 3+4+5+6, crispant 58); wmD, wholemount dorsal view; wmL, wholemount left-side lateral view; wmR, wholemount right-side lateral view; wmV, wholemount ventral view. #### File: Supplementary\_Files\_1-3\_Foxg1.zip **Description:** Images in this folder (zip archive) underlie the *Foxg1* crispant data reported in Supplementary Table 1 of the preprint, the *Foxg1* crispant data plus data from uninjected siblings/half-siblings reported in **Supplementary File 1** of the paper (Breakdown by sgRNA mix of CRISPR/Cas9 experiments) and the *Foxg1* crispant data reported in **Supplementary File 3** of the paper (Breakdown by individual crispant of *Foxg1* crispant phenotypes). Image files are organised into subfolders based on the sgRNA mix used, with a separate subfolder for the uninjected siblings/half siblings), and the ISH marker analysed (*Cacna1d, Kcnab3, Mafa, or* Neurod4). Within each subfolder, images of *Foxg1* crispants without a phenotype are included in a separate "no_phenotype" subfolder, where relevant. This matches the organisation of Supplementary File 3 of the paper. *Filenames in Supplementary_Files_1-3_Foxg1* Filenames include the CRISPR/Cas9 target gene (Foxg1), sgRNA mix (sgRxxx) and a unique 3-digit code, or, for uninjected siblings/half-siblings, the batch number (ctrlBxx) followed by a unique 3-digit code (see section "Abbreviations in filenames" below). Filenames include the ISH marker used (Cacna1d, Kcnab3, Mafa or Neurod4) and "a-Sox2" if post-ISH immunostaining was performed with the anti-Sox2 antibody. Filenames end in a 6-digit date in yymmdd format (e.g., 211020). This corresponds to the date the ISH protocol was started. *Abbreviations in filenames:* Ar, *Acipenser ruthenus*; Ar45, *Acipenser ruthenus* stage 45; sgRxxx_yyy_, sgRNA mix plus 3-digit crispant code (e.g., sgR12_028\_ corresponds to sgRNA mix 1+2, crispant 28); ctrlBxx_yyy_, batch number plus 3-digit uninjected sibling/half-sibling code (e.g., ctrlB20_001\_ corresponds to batch 20, uninjected larva 001); wmD, wholemount dorsal view; wmL, wholemount left-side lateral view; wmR, wholemount right-side lateral view; wmV, wholemount ventral view.