Downloading scRNA-Seq data for mouse developing brain

Technical
1

Hello! I’m looking to download the RNA-Seq genecode normalized expression values and metadata for the mouse developing brain (shown in the heatmaps). This is available for download with the developing human brain but I cannot find any downloadable data for the mouse brain that has gene expression at different developmental time periods. Is this possible to download?

For reference - this is the link to the downloadable data for human developing brain: RNA-Seq Gencode v10 summarized to genes

Best,
Ellie

2

The Allen Developing Mouse Brain Atlas does not include RNA-seq data or single-cell gene expression. The heatmaps you’re seeing in the atlas reflect quantified in situ hybridization (ISH) signal across brain regions and developmental time points, rather than sequencing-based expression values.

However, you can download the quantified ISH expression data. We’ve provided instructions in this forum topic: API for Allen Developing Mouse Brain Atlas.

If you’re specifically looking for RNA-seq data for the developing mouse brain, you may want to explore the Brain Knowledge Platform Data Catalog, where you can find single cell sequencing datasets from the developing mouse brain. Here’s the link to the catalog pre-filtered for mouse and transcriptomics data: Catalog.