I have used syn21088596 (ROSMAP_assay_rnaSeq_metadata.csv), syn3191087 (ROSMAP_clinical.csv), syn21323366 (ROSMAP_biospecimen_metadata.csv), and syn18694015 (snRNAseqPFC_BA10_id_mapping.csv) files in an attempt to get bulkRNASeq count data for the same 48 individuals for which the snRNASeq experiments were performed.
So far, I have been able to match only 35 samples, out of which 8 have no metadata about the libraryBatch.
Can anyone assist me in retrieving the bulkRNA-Seq information, including both the count matrix and metadata for all 48 samples?
Created by Ritwiz Kamal ritwizkamal Hello @ritwizkamal,
Thanks for your question. I took a look at this dataset and I was able to map the projids found in the sample key file (syn21261601) to the projids in the ROSMAP_clinical.csv file (syn3191087). From here, I used the corresponding individual ID's to map to the ROSMAP_biospecimen_metadata.csv file (syn21323366). All 48 individual ID's mapped to the biospecimen metadata file. However, only 37 of these individuals seem to have "rnaSeq" assays available. At this point, my best guess is that the individuals selected for this study were chosen based on clinical pathology rather than overlap with previously generated RNASeq data. I'm tagging @hmathys here in case this is not correct.
For count data, I would recommend utilizing the [RNASeq Harmonization Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn21241740) which contains gene expression matrices for all available rosmap Bulk RNAseq samples, run through the same pipeline and aligned to the GRCh38 genome. Here is a link to the Rosmap data in this study: https://www.synapse.org/Synapse:syn22231797.
I hope this helps a little bit, but let me know if anything is unclear or if you have any other ideas.
Best,
Will
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Unable to match all 48 snRNASeq IndividualID or projid or subject to metadata from the bulkRNASeq (only 35 matches) page is loading…