DOI: 10.5061/dryad.41ns1rnr6
title: Data from: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2

description: The meninges act as a regulator of brain development by secreting ligands
 that act on neural cells to regulate neurogenesis and neuronal migration.
 Meningeal-derived retinoic acid (RA) promotes neocortical neural
 progenitor cell cycle exit; however, the underlying molecular mechanism is
 unknown. Here, we used spatial transcriptomics and profiling of
 retinoic-acid receptor-α (RARα) DNA binding in Foxc1-mutant embryos that
 lack meninges-derived ligands to identify the neurogenic transcriptional
 mechanisms of RA signaling in telencephalic neural progenitors. We
 determined that meningeal-derived RA controls neurogenesis by suppressing
 progenitor self-renewal pathways Notch signaling and the transcription
 factor Sox2. We show that RARα binds in the Sox2ot promoter, a long
 non-coding RNA that regulates Sox2expression, and RA promotes Sox2ot
 expression in neocortical progenitors. Our findings elucidate a previously
 unknown mechanism of how meningeal RA coordinates neocortical development
 and insight into how defects in meningeal development may cause
 neurodevelopmental disorders.
description: Pregnant mice were anesthetized using isoflurane and embryos were
 collected at E12, E13, or E14 by removing the heads and placing them in 4%
 paraformaldehyde (PFA) overnight at 4 degrees C. Whole heads were placed
 into 20% sucrose overnight and embedded in OCT. Mouse heads were sectioned
 at 12 um increments using a cryostat and sections mounted on glass slides.
 Sections were blocked in 3% bovine serum albumin (BSA) + 0.05% Triton-X
 for 1 h at room temperature and incubated with primary antibodies at a
 dilution of 1:100. Following incubation with primary antibody(s),
 sections were incubated with appropriate Alexa Fluor-conjugated secondary
 antibodies and DAPI (Invitrogen, Carlsbad, CA, United States). In situ
 hybridization was completed using the ACD Bio Multiplex Fluorescent
 Detection assay kit (Neward, CA) and their probes against Sox2 and
 Sox2ot.
description: # Meningeal-derived retinoic acid regulates neurogenesis via suppression
 of Notch and Sox2
 [https://doi.org/10.5061/dryad.41ns1rnr6](https://doi.org/10.5061/dryad.41ns1rnr6) ## Description of the data and file structure Images are czi, tiff, or jpeg extension and can be opened using ImageJ/Fiji. For czi, use the Bio-Formats plugin. **Figure 3**: In the subfolder "RNAscope" there are raw czi files for the samples Control, Control +RA (retinoic acid) treatment, Foxc1 mutant, Foxc1 mutant + RA with the RNAscope probe staining DAPI (channel 4), Sox2ot (channel 2) and Sox2 (channel 1). The corresponding single channel JPEG files are also in the folder.  **Figure 4**: Contents in zip file contain two folders: "Notch1 and Dll1" and "Sox2 and NICD". The "Notch1 and Dll1" subfolder contains individual JPEG images for Control, Control +RA treatment, Foxc1 Mutant, and Foxc1 Mutant + RA treatment for the following immunohistochemical stains: Dll1, Notch1 and merged. There are also the raw CZI files with DAPI (channel 3), Dll1 (channel 2), Notch1 (channel 3). In the subfolder "Sox2 and NICD", there are the individual JPEG images for Control, Control +RA treatment, Foxc1 Mutant, and Foxc1 Mutant + RA treatment for the following immunohistochemical stains: DAPI, Sox2, NICD, and a merged JPEG.  **Figure 5**: Contents in zip file are of the control and dominant negative RBPJ (dnRBPJ) jpeg images where cyan is the DAPI/Nuclei and yellow is the electroporated GFP cells.  **Supplementary Figure 1**: This folder contains the raw czi files of the control and Foxc1 Mutant meninges stains: DAPI (channel 4), Col1a1 (channel 3), and Raldh2 (channel 2). There are also two tile scans of the meninges with the staining: DAPI (channel 4), Crabp2 (channel 3), and Foxc1 (channel 2).