The ABC Atlas has been updated with new data!
The Developing Mouse - Visual Cortex taxonomy is derived from a single cell transcriptomic dataset containing 568,654 cells from 53 donors ranging in age from embryonic to adult.
This release is part of an initiative to create a high-quality atlas of cell types in the mouse visual cortex and thalamus across development using large scale single cell transcriptomic analysis. All of the cells in this dataset were collected from wild-type C57Bl6/j mice.
Cells were collected from at 25 time points spanning ages E11.5 to postnatal day 28 (P28). At ages E11.5 to E14.5 the entire brain was dissected and cells were prepared for sequencing using the 10x Genomics platform. At ages E15.5 to P28 we dissected out either visual cortex or thalamus and prepared cells for sequencing using the 10x Genomics platform. This dataset covers the visual cortex.
The cell-type assignment is a four level taxonomy defining 15 classes, 40 subclasses, 148 clusters and 714 subclusters. This cell-type assignment is broadly consistent with those from the previous studies from the Allen Institute for Brain Science, Whole Mouse Brain (WMB) and the Broad Institute whole mouse brain taxonomy at the subclass level while providing finer cell-type and temporal resolutions with additional subcluster annotations.
To generate this developing taxonomy, we applied the Quality Control (QC) and post-integration QC pipelines. Integration and label transfer of scRNA-seq between ages was performed using Seurat/scVI.
Explore this data now in the ABC Atlas!
Other resources related to this release:
- Check out our GitHub resources for programmatic access to this data and to learn more about the metadata included in this package including a detailed cell type annotation table, including hierarchical membership and anatomical localization..
- Map your own data to this taxonomy using MapMyCells.
- Additional information and other data related to this study is available through the Brain Knowledge Platform Data Catalog
- The related publication: Continuous cell-type diversification in mouse visual cortex development
As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.