Hello, We're excited to work with the AMP-AD 2.0 snRNA/ATAC-seq profiling of diverse donors (syn52339332) data! Thank you for making it accessible. I notice there is no RNA object for oligodendrocytes, but there is an "assaylist" object for the ATAC data. Is there an oligodendrocyte count matrix that can be added to the processed data folder, or should it be accessed another way? Thank you.

Created by David Gate gatelab
Thanks @vilasmenon! I'm going to add that to the methods description on the study page. Appreciate the help!
Hi @rrajesh and @abby.vanderlinden, the filtered objects contains nuclei that have >500 UMIs (based on RNA-seq), after running CellBender to remove background, and have also passed 4 rounds of clustering to remove potential doublet signatures. These doublet signatures were identified based on mixed expression of known broad class-specific genes in the brain.
Hi @rrajesh , according to the 10x Multiome methods section for this study, I believe the filtering was done with just the default parameters in the Cell Ranger ARC software: https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn51732482#Methods-10xMultiome. However, possibly @vilasmenon can verify if that's the case or if there were other filtering criteria!
Dear team, Could you please specify what are the conditions for the "filtered" cells in these count matrices and ATAC-seq files? To clarify my question, have these cells been only filtered to exclude background, duplicate etc. or have they also been filtered for UMI per cell etc. also? Thanks. Best regards, Rajesh
Hi @gatelab, the oligodendrocyte RNAseq counts file is now available publicly here: https://www.synapse.org/#!Synapse:syn55446335. Thanks @vilasmenon for your help!
Good observation - the oligodendrocyte RNAseq counts file somehow did not upload properly. We will get it up there in the next couple of days.
Hm, good catch -- it does seem like there should be a count matrix for oligodendrocytes. @vilasmenon, any chance there is an snRNAseq counts matrix for oligodendrocytes from the Diverse Cohorts 10x multiome study that we missed uploading?

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