Data from: Cohesin protein Smc3 influences kinocilial structure and function
Data files
Dec 02, 2025 version files 3.37 GB
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Figure_1_Data.zip
961.70 MB
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Figure_2_data.zip
516.14 MB
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Figure_3_Data.zip
1.37 GB
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Figure_4_Data.zip
18.94 MB
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Figure_S1_data.zip
1.70 MB
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Figure_S3_Data.zip
503.78 MB
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README.md
9.74 KB
Abstract
Cohesinopathies and ciliopathies are congenital disorders affecting overlapping body systems. The extent to which these syndromes may be linked remains largely untested. Recently, reduced expression of a cohesin core subunit, Smc3, was found to result in abnormal otolith development in zebrafish embryos. This finding suggests that Smc3 may contribute to kinociliary development and function, which would represent a novel role for Smc3. Using hair cells found in neuromasts of the posterior lateral line, we found that Smc3 knockdown resulted in reduced kinociliary length. To address the role of Smc3 in kinocilial function, we monitored neomycin resistance of neuromasts (associated with several cilial gene mutants) and FM1-43X uptake in hair cells (associated with mechanotransduction). We found that Smc3 knockdown indeed led to neomycin resistance of the posterior lateral line neuromasts, suggesting impaired kinocilium function. However, neuromast hair cells did not have defects in FM1-43X uptake. We further demonstrated that hair cell number is reduced within neuromasts. This study suggests a significant influence of cohesin subunit Smc3 in ciliary structure and function and provides a preliminary link between cohesinopathy and ciliopathy etiologies.
Dataset DOI: 10.5061/dryad.5dv41nsk3
Description of the data and file structure
This dataset includes image files captured and quantitative analysis performed to discern the influence of cohesin protein Smc3 on kinociliary structure and/or development in zebrafish larvae. Datasets are organized in separate .zip files for separate experimental efforts corresponding to each figure in the manuscript. Each .zip file contains additional README files with details to provide necessary information.
Files and variables
File: Figure_1_Data.zip
Description: This .zip file contains .tiff files of each imaged and evaluated neuromast for kinociliary length analysis. Folder names indicate the injection type. The dataset includes .tiff files of observed neuromasts used for kinociliary length analysis. Each file name corresponds directly to the identifiers used in the .csv file for that injection type.
The .csv file contains measurements of a representative kinocilium from the indicated neuromast and calculations to estimate the length of the kinocilium based on the measurements.
Variables within each .csv file are defined as described below:
Name: corresponds to the name of the file from the dataset analyzed in that row.
First z slice: indicates the image within the z-stack where the longest kinocilium first appears.
Last z slice: indicates the image within the z-stack where the longest kinocilium last appears.
z-thickness: indicates the thickness, microns, of each image within the stack.
z-displacement: calculation of the displacement, in microns, of the longest kinocilium in the z-dimension.
First x: indicates the x-coordinate where signal from the kinocilium in the first z slice occurs.
Last x: indicates the x-coordinate where signal from the kinocilium in the last z slice occurs.
x-displacement: calculation of the displacement, in microns, of the longest kinocilium in the x-dimension.
First y: indicates the y-coordinate where signal from the kinocilium in the first z slice occurs.
Last y: indicates the y-coordinate where signal from the kinocilium in the last z slice occurs.
y-displacement: calculation of the displacement, in microns, of the longest kinocilium in the y-dimension.
2D displacement: calculation of the displacement, in microns, of the longest kinocilium in x and y dimensions.
Ciliary length: calculation of the displacement, in microns, of the longest kinocilium in x, y and z dimensions.
File: Figure_2_data.zip
Description: ## Overview
This dataset contains image and analysis files related to neuromast imaging and hair cell quantification.
## File Types
- .czi files: These are the raw image files acquired directly from the microscope.
- .tiff / .mp4 files: These are converted versions of the raw data, exported for ease of viewing and compatibility with analysis software.
## Required Software
To open and view the proprietary .czi files, use ImageJ or Fiji (which includes the Bio-Formats plugin). Both programs are freely available and widely used for microscopy data visualization and analysis.
## Data Conversion
Raw .czi files were exported either as TIFF or MP4 formats using standard export functions within the imaging software. No additional processing or filtering was applied during conversion.
## Imaging Notes
Not all neuromasts were imaged for every embryo due to time constraints during acquisition. However, all imaged neuromasts are representative of the overall population and were selected to ensure consistent sampling across embryos.
## Quantification Data
The accompanying Excel file includes raw hair cell counts, recorded manually while observing each embryo under the microscope. These values serve as the primary quantitative dataset corresponding to the imaging files.
## Definition of Excel Column Header Variables
Name: larvae were identified by SC KD or Smc3 KD, indicating whether they had received a standard control (SC) or Smc3 (Smc3) morpholino injection at the one cell stage and a number to differentiate the sample from others of the same injection type.
MI1: number of hair cells observed in the middle 1 neuromast.
MI2: number of hair cells observed in the middle 2 neuromast.
O2: number of hair cells observed in the otic 2 neuromast.
M2: number of hair cells observed in the mandibular 2 neuromast.
IO4: number of hair cells observed in the infraorbital 4 neuromast.
Average: a calculation of the average number of hair cells observed across the 5 evaluated neuromasts for each larva.
File: Figure_3_Data.zip
Description: The dataset includes .tiff images of 3dpf embryos from which neuromasts were counted following control treatment or neomycin treatment. For some embryos, a series of images at different microscope focuses were captured in an effort to visualize all observe neuromasts, indicated by the decimal series in the file name (5 dpf scmo control 15.1.tif and 5 dpf scmo control 15.2.tif are unique images of the same embryo).
The .csv files indicate the number of observed neuromasts in each embryo. The embryo name in the .csv file corresponds to the number of the embryo indicated by the .tif file names.
Variables within each .csv file are defined as described below:
Name: corresponds to the name of the file from the dataset analyzed in that row.
Observed neuromasts: corresponds to the number of neuromasts observed in that sample number.
File: Figure_4_Data.zip
Description: The dataset includes maximum projection .tif files of neuromasts used for quantitative analysis, as indicated in the accompanying .csv files. Each .tif file name corresponds directly to the identifiers used in the .csv files.
The .csv files contain measurements of the mean intensity of an ROI drawn around the neuromasts, the mean intensity of the background of each image, and the ratio of ROI to background mean intensity.
Outlier ROI/background ratios were excluded from the analysis if they fell above or below the interquartile range. Inclusion or exclusion of each ROI/background value from analysis is indicated in the .csv files. Excluding outliers did not change the results of statistical analysis.
Variables within each .csv file are defined as described below:
Name: corresponds to the name of the file from the dataset analyzed in that row.
ROI mean intensity: average intensity of all pixels falling inside the region of interest drawn in ImageJ around the cells comprising the neuromast.
Background mean intensity: average intensity of all pixels falling inside the background region drawn in imageJ in the background of each image.
ROI/background: ratio of the “ROI mean intensity” value divided by the “Background mean intensity” value.
Excluded from analysis due to falling outside of the IQR?: indicates whether the value was included in final analysis for the construction of Figure 4 in the publication based on the value falling outside of the interquartile range. Exclusion of these values did not change the results of analysis.
File: Figure_S1_data.zip
Description: The dataset includes lanes that were used for quantitative analysis, as indicated in the accompanying Excel file. Each lane label corresponds directly to the identifiers used in the Excel sheet.
The Excel file contains measurements of pigment intensity, along with normalized values relative to the designated right-hand control sample.
Certain lanes were excluded from the analysis due to quality control considerations. Common reasons for exclusion include insufficient initial protein quantity, evidence of protein degradation, or other technical issues affecting data reliability.
## Definition of Excel Column Header Variables
Dpf: days post fertilization
Name: indicates the identifier used for each sample, identified by SC KD or Smc3 KD, indicating whether they had received a standard control (SC) or Smc3 (Smc3) morpholino injection at the one cell stage and a number to differentiate the sample from others of the same injection type.
Smc3: intensity value for the Smc3 protein band measured using ImageJ normalized to the background
Tubulin: intensity value for the Tubulin protein band measured using ImageJ normalized to the background
Normalized value: Normalized value of Smc3 intensity to tubulin intensity within the same sample
Average % reduction: Normalized Smc3 value of standard control − Normalized Smc3 value of in Smc3 KD/Normalized Smc3 value of standard control×100
Normalized to SC: Value of Smc3 intensity of all samples normalized to SC samples
File: Figure_S3_Data.zip
Description: The dataset includes .tiff images of 3dpf embryos from which somites were counted. A series of images at different microscope focuses were captured of each embryo, indicated by the lettering series in the file name (ex. 72hpf_SCKD_1-A.tif and 72hpf_SCKD_1-B.tif are unique images of the same embryo).
The .csv files indicate the number of somites observed in each embryo. The embryo name corresponds to the number of the embryo indicated by the .tif file names.
Variables within each .csv file are defined as described below:
Name: corresponds to the name of the file from the dataset analyzed in that row.
Somites: number of somites observed for that sample.
Code/software
To open and view the proprietary .czi files, use ImageJ or Fiji (which includes the Bio-Formats plugin). Both programs are freely available and widely used for microscopy data visualization and analysis.