Data and code from: Evidence for chronological diversification of spinal neuron subtypes by a shared sequence of transcription factors
Data files
Feb 27, 2026 version files 92.46 MB
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Input_data_Caudet_Segarra_et_al.zip
92.45 MB
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README.md
8.27 KB
Abstract
The mechanisms underlying the generation of the immense diversity of neuronal cell types remain a fundamental question of developmental biology. In the spinal cord, different “cardinal classes” of neurons that share a common molecular identity are produced from spatially segregated progenitor domains. Within many such classes, a stereotyped sequence of divergent neuronal types of related function is generated over time, raising the question of the molecular mechanisms that control this process. Here, we show that the successive expression of mouse transcription factors Onecut2, Pou2f2, and Pou3f1 within the cardinal classes giving rise to motor and sensory circuits, correlates with the emergence of sequentially generated subpopulations of neurons within those domains. We demonstrate that the genetic loss of Pou2f2 results in impaired development of two early-born motor neuron columns and re-specification of anterolateral system projection neurons as a later-born subset. Similarly, we show that Pou3f1 expression is required for the normal development of later-born subsets of motor neurons and anterolateral system projection neurons. Together, our observations provide functional evidence that horologic diversification of output neurons of spinal motor and sensory circuits are driven by a conserved sequential order of expression of transcription factors.
Dataset DOI: 10.5061/dryad.j3tx95xtz
Description of the data and file structure
This repository contains all data and the R code to reproduce the plots in Figures 1-7 and S1-S9 + S15 from Caudet Segarra et al. 2025.
Files and variables
Data files hosted by Dryad
- Input_data_Caudet_Segarra_et_al.zip
Software files hosted by Zenodo
- Supplemental_Experimental_Procedures_-_Imaging_Revision.Rmd
- Supplemental_Experimental_Procedures___Revision_scRNAseq.Rmd
Supplemental files hosted by Zenodo
- Output_Caudet_Segarra_et_al.zip
Description: Please unpack Input_data_Caudet_Segarra_et_al.zip file and download the R scripts Supplemental_Experimental_Procedures_-_Imaging_Revision.Rmd and Supplemental_Experimental_Procedures___Revision_scRNAseq.Rmd from Zenodo and put them in the same directory as the input data. There should be 2 R Markdown files (called Supplemental Experimental Procdures - Imaging_Revision.Rmd and Supplemental Experimental Procedures - Revision scRNAseq.Rmd), 2 Input folders (Input and Input_scRNAseq) and 2 Output folders (Output and Output_scRNAseq).
Running the scripts in the R Markdown files should generate all the data shown in the manuscript. Output data was also uploaded as Supplemental files to Zenodo.
Quantitative image analysis
The Input folder contains all data files underlying quantitative image analysis performed in Figures 1-7 and S1-S9 and S15 organized by figures. The code provided in Supplemental Experimental Procdures - Imaging_Revision.Rmd should load these files and generate all plots provided in the main text and supplemental figures and save them to the output folders.
Data in the input folder is organized by figures. Subfolders in each figure folder are organized by stainings. Subfolder names indicate the staining date, genotype + stage, and the order of channels during image acquisition. Identity of the fluorophores used for fluorescent detection is also indicated in most cases (e.g. 647Foxp1 indicates that Foxp1 was detected with an Alexa647-conjugated secondary antibody). Staining folders in figure folders 'Figure1+S1', 'Figure2', 'Figure3+4', 'Figure5,6,7', 'Figure7', 'FigureS2', 'FigureS4', 'FigureS8' and 'FigureS15' contain .csv files containing the data underlying the quantititive image analysis.
Unless specified otherwise, .csv files contain the following columns:
- Area: Area of the segmented nucleus in Pixels
- Mean: Mean fluorescence intensity of the nucleus
- XM: X coordinate for centre of mass of the nucleus
- YM: Y coordinate for centre of mass of the nucleus
- Ch: Imaging Channel
Some .csv files contain additionally the columns:
- Min: Minimal pixel intensity detected per nucleus (not used for further analysis)
- Max: Maximal pixel intensity detected per nucleus (not used for further analysis)
Intensity profile plots in Figures 5E and S8E were generated based on .csv files provided in folders 'Figures5,6,S7/240612_SC_e10.5_405Pou2f2_488Lhx3_568Isl1-2_647Foxp1_slide1401' and 'FigureS8/250717_SC_Nes-Cre_R26-YFP_e10.5_450Pou2f2_488GFP_568Isl1-2_647OC2_slide2429B' and 'FigureS8/250717_SC_Nes-Cre_R26-YFP_e10.5_450Pou2f2_488GFP_568Isl1-2_647Cre_slide2429A'. On each section, independent line profiles for the left and right hemisection were generated using Fiji's 'PlotProfile' function of a 200 µm wide line.
.csv files containing data underlying intensity profile plots contain the following columns:
- Distance: Distance along the profiles, starting at the ventricular zone (= data in columns X1, X2, X3, X4, X5, X6, X7)
- Value: Intensity value of Channel1 along profile 1
- Y1: Intensity value of Channel2 along profile 1
- Y2: Intensity value of Channel3 along profile 1
- Y3: Intensity value of Channel4 along profile 1
- Y4: Intensity value of Channel1 along profile 2
- Y5: Intensity value of Channel2 along profile 2
- Y6: Intensity value of Channel3 along profile 2
- Y7: Intensity value of Channel4 along profile 2
Dynamics of Foxp1 and Mecom positive MNs are provided as Excel sheet in 'Figures5,6,S7/S7F_Foxp1_Mecom_timecourse.xlsx'. Sheets within the Excel file contain data from the different developmental stages (e9.5, e10.5, e11.5, e12.5).
The Excel file contains the following columns:
- % Foxp1: Percentage of motor neurons expressing Foxp1
- % Mecom: Percentage of motor neurons expressing Mecom
Cell counts of Isl1 Mecom+ MMC neurons expressing Pou2f2 and Pou3f1 (Figure 5K) are provided in the folder 'Figures5,6,S7/230510_SC_e11.5_405Pou2f2_488Pou3f1_568Mecom_647Isl1_slide734B' as .csv file.
The .csv file contains the following columns:
- embryo : ID of the quantified embryo
- Isl1 Mecom+: Total number of Isl1 Mecom+ MMC neurons
- Pou3f1+: Number of Pou3f1-positive MMC neurons
- Pou2f2+: Number of Pou2f2-positive MMC neurons
Fraction of motor neurons in thoracic motor columns expressing Pou2f2 and Pou3f1 is provided as .csv file in 'Figure5,6,S7/221012_SC_e11.5_405Pou2f2_488Isl1-2_568Pou3f1_647Foxp1/Quantifications_Pou2f2_Pou3f1_thoracic_MNs.csv'
The .csv file contains the following columns:
- PGC_Pou2f2: Fraction of PGC neurons expressing Pou2f2
- PGC_Pou3f1: Fraction of PGC neurons expressing Pou3f1
- HMC_Pou2f2: Fraction of HMC neurons expressing Pou2f2
- HMC_Pou3f1: Fraction of HMC neurons expressing Pou3f1
- MMC_Pou2f2: Fraction of MMC neurons expressing Pou2f2
- MMC_Pou3f1: Fraction of MMC neurons expressing Pou3f1
Data underlying the quantification of fraction of nuclei labelled by EdU administration at e9.5 or e10.5 expressing Onecut2, Pou2f2 and Pou3f1 are provided in Excel files in 'FigureS4/IF168_25013_e13.5_SC_488Zfhx3_Cy3Pou2f2_647EdU'. Each sheets in the Excel file correspond to data from one embryo section.
The sheets contain the following columns:
- Area: Area of the segmented nucleus in Pixels
- Mean: Mean fluorescence intensity of the nucleus
- Min: Minimal pixel intensity detected per nucleus (not used for further analysis)
- Max: Maximal pixel intensity detected per nucleus (not used for further analysis)
- Ch: Imaging Channel
Some sheets contain additionally the columns:
- XM: X coordinate for centre of mass of the nucleus (not used for further analysis)
- YM: Y coordinate for centre of mass of the nucleus (not used for further analysis)
Outlines of spinal cord sections used to quantify the mediolateral distribution of Onecut2+, Pou2f2+ and double-negative Phox2a neurons in Figure 7 are provided as .tif in the folder 'Figure7/IF115_e12.5_Pou2f2_Lmx1b_Phox2a_OC2'. Each .tif is in a subfolder, whose name matches the .csv files provided in 'Figure7/IF115_e12.5_Pou2f2_Lmx1b_Phox2a_OC2'.
Single-cell RNA sequencing
To reproduce the scRNAseq analysis, first the object m_neural.rds needs to be generated as specified in Delile et al. 2019, Development, and https://github.com/juliendelile/MouseSpinalCordAtlas. For analysis of scRNAseq from Wang et al. 2022, Nat. Comm., please download the data from the GEO repository (GSM4734731) and put it into the Input_scRNAseq folder. For data from Bell et al. 2024, PNAS, please download GSE240528FinalObject.Robj, provided via the GEO repository (GSE240528) and put this object into the the Input_scRNAseq folder.
Code/software
Data was analyzed using R 4.1.2 using R Studio version 2025.09.0+387 (2025.09.0+387). For some parts of the code Python version 3.8.15 was loaded via the R package reticulate. A complete list of the utilized R packages/libraries is provided at the end of the PDFs generated from the provided R Markdown documents.
Access information
Other publicly accessible locations of the data:
- Input data for the scRNAseq analysis is partially available from the GEO repository (GSM4734731, GSE240528)
Data was derived from the following sources:
- The object m_neural.rds needs to be generated as specified in Delile et al. 2019, Development, and https://github.com/juliendelile/MouseSpinalCordAtlas.
