how to get visium HD dataset with its information

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11 weeks ago

Ibrahim • 0

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?

spatial visiumHD transcriptomics scanpy • 346 views

ADD COMMENT • link updated 11 weeks ago by Nat.Nataren ▴ 100 • written 11 weeks ago by Ibrahim • 0

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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.

ADD REPLY • link 11 weeks ago by GenoMax 148k

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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

ADD REPLY • link 11 weeks ago by Nat.Nataren ▴ 100

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