Hunting down the extended atlas

[dagarfield]

Hello!

Big fan of the paper and the atlas. I was wondering if you could help me to locate the Extended atlas version of the data referenced on the intro page to this gitlab? In the CellxGene references, it appears (no matter which one you select) that you get the standard atlas.

Thanks!

[gokceneraslan]

Related question is why Smillie et al., Cell, 2019 was mentioned on the github readme but it seems missing in the Extended atlas?

[amandaoliver15]

Hi @dagarfield, thanks for the interest in our paper and atlas. It's strange you're getting the same atlas regardless of which link you click, this doesn't happen for me. Could you try clearing your cache (control + f5 for PC or command + shift + R for Mac) and try the interactive viewer links again?

Hi @gokceneraslan, apologies for the confusion here. In our paper we added epithelial cells from Smillie et al. to look for metaplastic cells in the large intestine (Extended data 6i-k). We forgot to add this object into the download link but have just made it available for download (30_Extended_Pan-GI_atlas_Epi_LI_AP_withcountsmatrices_20241119.h5ad or .rds). In our atlas we mainly started from raw data which we reprocessed, unfortunately we did not include data from Smillie et al. Cell 2019 and some other datasets because of data access issues. The cases where we added additional data from count matrices (eg. Kong et al. Immunity 2023) was to improve coverage of epithelial cells and to answer specific biological questions. There are already efforts for a v2 Gut Cell Atlas which will include Smillie along with additional published and unpublished data. I hope the epithelial data from Smillie et al. will help you and please let me know if anything I mentioned isn't clear.

Thanks, Amanda