I wanted to confirm that the metadata file in Mouse Whole Cortex and Hippocampus 10x dataset is up to date. I noticed that there is consistency between the data in the metadata table and the Shiny app (https://taxonomy.shinyapps.io/ctx_hip_browser/); which one is up to date?
The data between the Mouse Whole Cortex and Hippocampus 10x datasets (linked here) and the above taxonomy browser should match right now because (from the Cell types page): “NOTE As of 10/21/2021: The Mouse CTX-HPF datasets have been updated to reflect the final taxonomy and cell type annotations from the May 2021 paper in Cell here.”. If you’ve downloaded the data more recently than that, and they still don’t match, please reply here and we’ll look into it.
Thanks for the reply. Yes, I downloaded the metadata.csv file a few days ago. Some clusters exist in the metadata file and don’t exist in the taxonomy browser. Also, some matched clustered (cluster 6, for instance) are shown as 100% in HIP in taxonomy browser while they have samples in multiple regions in the metadata file (actually HIP is less than 40% in the metadata file).
As mentioned there was an update to Mouse CTX-HPF dataset on brain-map.org to match the paper published in Cell. With that there was an update to the ShinyApp as well: https://taxonomy.shinyapps.io/ctx_hip_browser_v2 . The taxonomy in the old ShinyApp link reflects a previous version of manuscript that can be found on bioRxiv.