how to get visium HD dataset with its information
I'm looking for visium HD spatial data from cancer samples. I need information about the sample, such as cancer stage, region, pathological annotation, and so on. Where can I get that type of data with that information?
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Nat.Nataren •
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Genomancer •
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Depending on how much of that information is personally identifiable you may not be able to get the metadata unless you get approval from dbGaP and/or the project that has such data. Getting access to images would be another hurdle. SRA does not have a good way to accommodate this type of information.
Searching https://sra-explorer.info using
visium[All Fields] AND ("Cancer"[Organism] OR cancer[All Fields])brings up over 500 results. Start with that.Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the additional metadata you are after:
https://cellxgene.cziscience.com/datasets