Mouse Inhibitory Neuron Development

This webserver accompanies this publication:

Bright, Kotlyarenko & Neuhaus et al. 2025

About this resource

This browser enables interactive exploration of published single-cell RNA sequencing datasets covering mouse forebrain development, with a focus on inhibitory neuron populations.

It includes:

• Embryonic datasets from Bright, Kotlyarenko & Neuhaus et al. (2025), Di Bella & Habibi et al. (2021) and Bandler, Vitali & Delgado et al. (2022).
• Neonatal dataset from Bandler, Vitali & Delgado et al. (2022).

Together, these datasets span key stages of inhibitory neuron specification, migration, and maturation, across both dorsal and ventral forebrain structures. The browser provides access to gene expression profiles and gene regulatory network predictions.

We provide the following panels to explore our data:

• Dataset UMAPs: Explore structure of single-cell RNA-seq datasets. Visualize cell clusters, cell classes, developmental stages, experiments and studies. The data stems from this study and two additional datasets: Development of inhibitory neurons from Bandler, Vitali & Delgado et al. (2022) and development of excitatory neurons in somatosensory cortex from Di Bella & Habibi et al. (2021).
• RNA expression: Visualize expression of a gene of interest. UMAP plots can be split by cell cluster, cell class, developmental stage, experiment and study.
• Tracks: Data from scATAC-seq and NFIB CUT&RUN experiments can be explored in UCSC genome browser.
• Network: Explore interactions between up to 3 TFs and their direct target genes. Gene-regulatory networks were precdited using SCENIC+: González-Blas & De Winter et al. (2023).

If you want to discuss the biological context of the dataset, have questions, or would like to suggest features, feel free to join our open Matrix room. For more information please visit our lab website mayerlab.net.

Source code for this app is available on Github.