I would like to examine gene expression in human skeletal tissue or osteoclasts. However, dna_model.output_metadata only contains bone marrow tissue, and the output type is limited to hCAGE, with no osteoclasts available. How can I proceed with further exploration in this area?
Hi There!
Thanks for reaching out.
We have the following navigating data ontologies Colab notebook that has a table of all our metadata, and you can programatically interact with this data using an API key, or indeed download as a CSV.
Search using Ontology CURIEs: You can also search for specific ontology identifiers such as UBERON:0001134 (skeletal muscle tissue) which should have total RNA-seq data. Or for primary cells consider CL:0000515 (skeletal muscle myoblasts), CL:0000594 (skeletal muscle satellite cell), or CL:0002540 (mesenchymal stem cell of the bone marrow).
Use Proxy Cell Lines: You can search for relevant cell lines as a proxy. HT1080 (fibrosarcoma) tracks have been successfully used to model variants associated with bone mineral density.