Hi!
Firstly, thank you for depositing data at syn52293417 for this project!
I am having trouble finding donor information that correlates with the barcodes in the processed files at Gene Expression (snRNAseq - 10x) processed under the MIT ROSMAP study. A file with barcode-donor mapping information and donor metadata (age, sex, etc) would be very helpful. Please let me know if I am missing something
Thank you for your time and help!
Best,
Valentina
Created by Valentina Zhang zhangval Hello,
This is a good question... they don't provide the needed ID (specimenID) to be able to look this up in a different metadata file that has this information. At a guess, all files in this folder (syn52293433) should be from the prefrontal cortex since there's a file called `PFC427_raw_data.h5ad` in there and the methods description for this data mentions the PFC. There's another folder of multi-region data (syn52383412) where the files are named by region, so if you need that data too, those will be easy to tell apart.
I hope that helps!
Jaclyn Hi Jaclyn,
Thank you so much! I was able to map the metadata successfully.
One last question - I didn't see metadata about brain region within the files. Would there be a place where I could go to deduce the brain region that each barcode/sample came from?
Thanks!
Valentina Hello,
I've just taken a look at this and I think I figured it out. In the metadata of the Seurat object, there's a `projid` column, where each unique `projid` maps to a single individual. Since the cell barcodes are the rownames of the metadata, this should give you a barcode -> individual mapping. Then, you should be able to map this to the `projid` column of this metadata file: syn3191087 to get clinical data like age, sex, etc on each individual.
If you try this and it's still not mapping correctly, reply here to let me know!
Jaclyn Hi Jessica,
Thank you for your response. I have looked at the barcode-donor mapping at ROSMAP_snRNAseq_demultiplexed_ID_mapping.csv, but do not find the barcodes contained within the Seurat object I downloaded. For instance, I downloaded Vasculature_cells.rds (syn52368904), which gave me an object with barcodes like "GACTACAAGGCTCTTA-1-0". I was unable to determine their mapping to the ROSMAP donors. Could you please advise?
Best,
Valentina Hi Valentina,
My apologies for the delayed response to your questions, but I believe that the barcode-donor mapping file for ROSMAP donors is ROSMAP_snRNAseq_demultiplexed_ID_mapping.csv (syn34572333).
You can find the complete set of ROSMAP metadata files listed here: https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyData?Study=syn3219045#StudyMetadata
General information about working with metadata files is available in our help documentation: https://help.adknowledgeportal.org/apd/About-Metadata.2241626149.html
Please be aware that for ROSMAP, individual metadata is provided via ROSMAP_clinical.csv (syn3191087), which is backed by ROSMAP_clinical_codebook.pdf (syn3191090). Be aware that the metadata for ROSMAP, MSBB, and Mayo does not include a diagnosis column ? instead there are various values including Braak stages, CERAD scores, and sometimes cognitive dx info. In addition, we censor all ages >89 to reduce re-identification risk in our metadata. Furthermore, we only have a limited set of the full ROSMAP clinical data. Users who want uncensored ages or additional phenotypes should contact https://www.radc.rush.edu/ to request access to the extended data through them.
Best,
Jessica