Filliol, Aveline
Hello,
I am reaching out for guidance on how to submit large multiplex immunofluorescence datasets on the cbioportal.
We are in the process of submitting a manuscript that includes multiplex IF data generated from three human tissue TMAs (~300 cores encompassing 150 individuals of 2 different type of cancer), stained for 22 markers. Each channel is around 5–6 GB in size, and looking for to deposit these files on cbioportal.
Would Cbioportal would welcome and could you please advise on the best way to proceed with the upload of large files or direct us to someone who can assist?
Thank you very much for your help.
Best regards,
Aveline Filliol, PhD
Lead Program Manager
Scott Lowe’s lab
Sloan Kettering Institute
Memorial Sloan Kettering Cancer Center
415 E. 68th St. Box 373
New York, NY 10065
Phone: +1-646-888-3340
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de Bruijn, Ino
Hi Aveline,
Thanks so much for reaching out! We can def support visualization of multiplex IF data
We have a few examples that show the Minerva viewer within cBioPortal, see e.g.:
- Ovarian MSK SPECTRUM study, example case
- Orion colorectal: example case
- Breast OHSU: example case (hover over the imaging icon in the timeline and click on it). This is a more curated story of the image highlighting particular channels as you step through it
Allowing download of the data is more complicated, but we can discuss further
How about we find a time to chat next week? Let me know what works for you. I’m moving the google group to BCC
Thanks!
Ino
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