Data from: Modeling MPPH syndrome in vivo using Breasi-CRISPR
Data files
May 21, 2026 version files 34.07 GB
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Figure_1.zip
280.75 MB
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Figure_2.zip
7.86 GB
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Figure_3.zip
25.93 GB
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README.md
3.65 KB
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Tabular_Data_TSV_files.zip
662.82 KB
Abstract
The increasing availability and affordability of genetic testing have resulted in the identification of numerous novel variants associated with neurodevelopmental disorders. There remains a need for methods to analyze the functional impact of these variants. Some methods, like expressing these variants in cell culture, may be rapid, but they lack physiologic context. Other methods, like making a whole-mouse model, may provide physiologic accuracy, but these are costly and time-consuming. We recently developed a technique, Breasi-CRISPR (Brain Easi-CRISPR), which results in efficient genome editing of neural precursor cells via electroporation of CRISPR-Cas9 reagents into developing mouse brains. Since Breasi-CRISPR is extremely rapid and enables the analysis of targeted genes in vivo, we wondered whether this technique would accelerate the study of monogenic neurodevelopmental disorders. Here, we use Breasi-CRISPR to model megalencephaly postaxial polydactyly polymicrogyria hydrocephalus (MPPH) syndrome. We found that 2 days after Breasi-CRISPR, we were able to see neurodevelopmental phenotypes known to be associated with MPPH syndrome, including increased cyclin D2 protein abundance and an increase in neural progenitor proliferation. Thus, Breasi-CRISPR can efficiently model MPPH syndrome and may be a powerful method to add to the toolbox of those investigating the functional impact of patient variants in neurodevelopmental disorders.
Dataset DOI: 10.5061/dryad.8sf7m0d4c
Description of the data and file structure
All the data is from fluorescence microscopy, acquired as described in the materials and methods section of the paper.
Files and variables
Each compressed file contains all the processed and raw data used to generate the graphs in the figure.
- Figure_1.zip contains raw *.ND2 files (original acquisitions in NIKON's proprietary format), processed images (rotated and crop images used for quantification), *.XML files (generated by the Fiji Cell Counter Plugin), and an Excel file containing all the quantifications.
- Figure_2.zip contains two subfolders, one for the Ccnd2hi graph, and one for the signal intensity profile in the figure. The "Signal Intensity Profile" folder contains raw *.ND2 files and (original acquisitions in NIKON's proprietary format), CSV files generated via the "Plot Profile" function of Fiji, an Excel file containing all the quantifications, and a Graphpad Prism used to generate figures and statistics. The "Ccnd2hi cell counting" folder contains raw *.ND2 files and (original acquisitions in NIKON's proprietary format), processed images (rotated and crop images used for quantification), *.XML files (generated by the Fiji Cell Counter Plugin), and an Excel file containing all the quantifications.
- Figure_3.zip contains 3 folders for each graph panel in the figure. "2B" and "2C" contain raw *.ND2 files (original acquisitions in NIKON's proprietary format), processed images (rotated and crop images used for quantification), *.XML files (generated by the Fiji Cell Counter Plugin), and an Excel file containing all the quantifications. 2D contains raw *.ND2 files (original acquisitions in NIKON's proprietary format), zip ROI files used for measurements, and an Excel file containing all the quantifications. At the root, you will also find a Graphpad Prism used to generate graphs and statistics.
- Tabular_Data_TSV_files.zip contains the raw tabular data in the Excel files in a non-formatted, machine-readable format (tab delimited *.TSV files).
Excel Files Structure
The excel files each contain the following worksheets:
- "Raw Data"
- "Pivot table"
- "Normalized data": for each experiment (see below), some data were normalized over the average of the results observed in control conditions.
Raw data files naming convention
Naming of raw data files follows the following convention: IUE#_slide#_Brain#_Sec#_IF targets_objective magnification.
- IUE#: the identifier of the experiment. IUE stands for "in utero electroporation". IUECK means the experiment was performed by Claire Kittock. The absence of the "CK" suffix means the experiments was performed by LJ Pilaz. The experimental conditions associated with each brain can be found in the excel files containing the raw data for each graph.
- Slide#: the identifier of the slide on which the image section was.
- Brain#: the identifier of the analyzed brain. The conditions associated with each brain can be found in the excel files.
- Sec#: the identifier of the section on the slide (4-5 sections are mounted on each slide).
- IF targets: the proteins revealed by immunofluorescence on each image.
- Objective magnification: the magnification use for imaging.
Complete experimental details are available in the methods section of the associated manuscript.
Data from figure 4 is accessible in Gene Expression Omnibus Database: GSE302315.
