Still working on loading the data into our environments
PRECINCT01
Waiting on actual data files from UC Davis group
PANCAN01 (15 TB Re-analysis)
Submitter PoC identified
OSA02
Dawn & Sunetra are working on the template-driven data submission
Minutes (Not Verbatim)
**Voting for Iowa State submission, only samples that have RNA-Seq data for Bladder Cancer and Healthy individuals**
In favor: Greg, Erika, Roel, Warren
**Questions answered from email sent to submitters on 10//22**
The ICDC is comprised of cases of spontaneous arising cancer in canines. Is there some implied linkage between thyroid tumors and IBD?
We have 65 IBD tissues. Likely 10-20 healthy animals as "control" samples, with multiple tissues from each. Furthermore, these are biopsies of the intestinal site, and one of our papers is comparing things such as cell height and width of colon, ileum, duodenum in both healthy and diseased. Also, we have ~4 TCC bladder cancer organoid samples. About 30 samples of healthy organoids from various healthy organoids. To be honest, regarding "Is there some implied linkage between thyroid tumors and IBD?", I am not sure. We were comparing healthy and diseased tissue. If this answer is critical I can reach out to our veterinary who can better answers this.
How many of the 100 animals were controls?
Controls I assume you mean are healthy? If so the healthy animal number is above in answer #1.
Is there any molecular data available for these subjects or tissues?
For 2 animal organoids (six tissues each) there is bulk mRNA Seq data currently as a preprint on BioRxiv. Then 3 of the TCC bladder cancer organoids will have bulk mRNA Seq and Whole Genome Sequencing. I don't believe we have genetic data available for tissues.
The submission request form mentions 5 manuscripts being written based on the data, are any of these genomics or proteomics studies with molecular-level data?
In the answer above, one paper has RNA data, and the other paper will have DNA and RNA data.
Is there any clinical metadata available for these subjects (breed, age, sex, disease)?
Yes for the 65 IBD tissues we have the following metadata. (Sex, Date of birth, Breed, Weight, Disease state and more). For the healthy animals we have sex and age.
**Questions answered from email sent to submitters on 10/13/22**
How many of the canine patient samples will ultimately have omics data associated with them?
Currently we have 4 TCC bladder dog organoids that will have (mass spec for proteins, RNASeq, and whole genome DNA sequencing) published
Are metadata available for the cancer-related samples?
Yes metadata as in previous treatments, age, breed, sex, and some other patient history.
Are the organoids validated and are they available for other researchers?
We have multiple publications being released from our lab by the end of 2022 further validating these organoids as relevant canine models building on existing literature. Attached is one publication from our group of the original creation of canine intestinal organoids and a paper from our collaborator about canine bladder cancer organoids, where we are growing our own for chemotherapy testing.
Is there a long-term plan to have genomic coverage for all individuals?
For our TCC canine individuals I would say yes. For older cases we have slide scans from the dog likely has passed or it is not possible to sample, but moving forward we can begin to collect for that if interested.
Will these data be made accessible to the public in any other repository?
Currently we do not plan to post these 100+ slide scans anywhere else. We take screen captures of certain areas of the slide for our publications but the scans themselves will likely not be posted anywhere else.
**Q&A Session**
Will screening data be available in the future?
Depends on the contract, model is being developed by our lab, the model is owned by the lab
Are there publications?
There is RNA-Seq data from a publication that is currently in review. This would be available nearly immediately.
Will the organoids be made available to other researchers?
CRO approach, open to collaboration in the future.
As a researcher interested in testing a particular compound...
There would be a MTA and we would test the compound using our organoids and share data back with the NIH.
How do other labs reproduce research on the organoids?
There is a paper coming out that gives exact specifications, collaborations are possible, but the organoids would stay at Iowa State. Open to colloabortions with industry and academia.