Clarification on FACS datasets cell annotation

[geo2mandos]

Hello,

Thank you for this amazing data resource!

I have a question related to the cell annotation process for the FACS datasets.

1. After reading the supplementary files related to the treatment of tissues and the FACS process, I understand that cell surface markers were used to sort different subpopulations within each tissue.

2. However, in the methodology of the paper, it is mentioned that the Seurat pipeline for cell type marker gene based annotation of cells has been used for all datasets.

In the metadata files of the FACS dataset, one can find cell annotation files per tissue. How to interpret the content? Is it based on 1) or 2).

Maybe I missed this bit of information in the manuscript and supplementary materials.

Thank you in advance :)