I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data:
I am interested in using the SEA-AD dataset. I was wondering if you had anndata or seurat objects of processed snATAC-seq data, like the ones that you have given public access for the snRNA-seq data? Specifically, I am looking for the processed count data for the snATAC-seq as well as the snATAC-seq from the Multiome sequencing, to proceed with standard integration workflows such as those used in Signac. Could someone help me with my query? Any help is much appreciated.
We have available for the middle temporal gyrus an AnnData object on our AWS Open Data site which includes UMIs per peak for all cells (AWS S3 Explorer)
We do not yet have this available for the frontal cortex (DFC data).
Note that the MTG AnnData object has UMIs/peak for all cells, not the peaks called per subclass. For that you would need to subset the fragment file from our raw data on Sage Bionetworks AD Knowledge Portal (https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyData?Study=syn26223298) and use the cell annotations in the AnnData object to run the analysis.