Data for: Atoh1 is required for the formation of lateral line electroreceptors and hair cells, whereas Foxg1 represses an electrosensory fate
Data files
Sep 03, 2025 version files 11.67 GB
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README.md
10.34 KB
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Supplementary_File_1_Neurod4.zip
1.43 GB
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Supplementary_File_1_Tyr.zip
3.14 GB
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Supplementary_Files_1-2_Atoh1.zip
1.83 GB
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Supplementary_Files_1-3_Foxg1.zip
5.27 GB
Abstract
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.
Dataset DOI: 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).
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).
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.