Hello,
In the SEA-AD ATAC and multiome data generated are there any cell-type annotation or any cell-level metadata available that could be shared.
For the data set ATAC dataset syn26223298 do we have barcode metrics files available from the cellranger-atac required to carry out the barcode QC and filtering (i.e. peak_reahion_fragments, blacklisted regions). The directory does have cellranger processed fragments, but the barcode metrics are not available.
Thank you,
Rion
Created by Rion Pendergrass rkpendergrass Our Data and Technology team handle these uploads and the next data release is currently planned for the end of the year. In the interim, the metrics you want for each library can be pulled from the AnnData object in the AWS s3 bucket. -Kyle @lheath Thank you for providing the links for the various other datasets available.
@ktravaglini Thank you for providing me with the AWS S3 bucket link. If it's not too much trouble, could you please provide the summary metrics CSV files a bit sooner?
This would greatly assist us in completing some critical analysis using this dataset.
Thank you so much,
Rion Hello @rkpendergrass,
We have cell annotations and metadata for the snATACseq cells and their library level metrics for the MTG dataset in an AnnData object here: https://sea-ad-single-cell-profiling.s3.amazonaws.com/index.html#MTG/ATACseq/.
I just re-checked and you are correct that we did not upload the summary metrics CSVs for each library. I'll ask our Data and Technology Team to add these to our next data release manifest (likely towards the end of the year).
Best,
Kyle Hi @rkpendergrass,
This data comes from the Allen Brain Atlas, and they did not deposit their cell-type annotations here (the AD Knowledge Portal is only hosting the raw data for this project). They do host quite a lot of processed data on their [website](https://portal.brain-map.org/explore/seattle-alzheimers-disease/resources) related to the SEA-AD data, but I was not able to find a file with the cell-type mappings they performed for the ATACseq and multiome data. I wasn't able to find barcode metrics either, though they do have [processed ATACseq](https://portal.brain-map.org/explore/seattle-alzheimers-disease/seattle-alzheimers-disease-brain-cell-atlas-download?edit&language=en) files available.
@timdol , are celltype nomenclature mappings available for the ATACseq and multiome data on the SEA-AD website? And do you have the cellranger output needed for individuals to QC the raw data themselves? If it is available, can you please direct Rion to the appropriate resources?
Rion, the SEA-AD [Community Forum](https://community.brain-map.org/) is a good place to see if someone has asked your questions before, and also to submit questions if you don't have time to wait for an answer here. The folks at Allen Institute are quite responsive and helpful. Alternatively, for the cell-type annotations, you could use the user-friendly [MapMyCells](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells) tool on the Allen Brain Map website, which will assign their cell type nomenclature to any snRNAseq data matrix you provide.
I hope that helps (and thank you Tim for any light you can shed),
Laura
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