The 3C Content Committee has identified the following datasets that are being used in the tranSMART Platform. You will need to determine the availability and suitability of each dataset for your use. We have provided the information we know in the table. If you know of additional datasets, or have more information on any of these, please contact the Content Committee.
Public Datasets
These datasets have been loaded into the tranSMART Platform by one of the groups using the tranSMART Platform. In most cases, some curation was done to prepare the data for loading and may be required to use the data directly from the source.| Disease Area | Database or Study | Disease subset | Number of data sets or samples | Curated data sets available now | Licensed needed to download | Can be distributed to third parties |
|---|---|---|---|---|---|---|
| Oncology | TCGA | 30+ cancers | >10,000 samples | Rancho BioSciences | No for levels 3,4; yes for levels 1,2 | No |
| Oncology | CCLE | Various | >>10,000 samples | Rancho BioSciences | No | Yes |
| Oncology | Cosmic | Various | >>10,000 samples | No | Yes | |
| Oncology | GEO | Various | >400 | Rancho BioSciences | No | Yes |
| Oncology | ICGC | Various | >50 | Yes | No | |
| Oncology | GTEx | Normal tissues | >>1,000 samples | Yes | No | |
| Immunology | GEO | All | >100 | Rancho BioSciences | No | Yes |
| Immunology | GEO | IBD (Crohn’s, UC) | >35 | Rancho BioSciences | No | Yes |
| Immunology | GEO | IPF | >15 | Rancho BioSciences | No | Yes |
| Immunology | GEO | Lupus | >11 | Rancho BioSciences | No | Yes |
| Immunology | GEO | Misc (Kawasaki, Lyme, etc) | 10 | Rancho BioSciences | No | Yes |
| Immunology | GEO | RA, including psRA | 20 | Rancho BioSciences | No | Yes |
| Immunology | GEO | Sarcoidosis | 10 | Rancho BioSciences | No | Yes |
| Immunology | GEO | Vasculitis | 6 | Rancho BioSciences | No | Yes |
| Immunology | dbGaP | IBD (Crohn’s, UC) | 5 | Yes | No | |
| Immunology | dbGaP | IPF | 1 | Yes | No | |
| Immunology | dbGaP | Lupus | 2 | Yes | No | |
| Immunology | dbGaP | Scleroderma | 1 | Yes | No | |
| Immunology | EBI | all | >100 | Rancho BioSciences | Yes | No |
| Respiratory | GEO | >10 | Rancho BioSciences | No | Yes | |
| Respiratory | ECLIPSE | Unclear | Not known | |||
| Neurosciences | GEO | Alzheimer | >3 | Rancho BioSciences | No | Yes |
| Neurosciences | GEO | MS | 30 | Rancho BioSciences | No | Yes |
| Neurosciences | GEO | Parkinson | 7 | Rancho BioSciences | No | Yes |
| Neurosciences | dbGAP | Alzheimer | 4 | Yes | No | |
| Neurosciences | dbGAP | MS | 2 | Yes | No | |
| Neurosciences | dbGAP | Parkinson | 6 | Yes | No | |
| Neurosciences | ADNI | Alzheimer | >800 samples | Yes | No | |
| Neurosciences | PPMI | Parkinson | >600 samples | Yes | No | |
| Neurosciences | LRRK2 | Parkinson | >800 samples | Yes | No | |
| Neurosciences | BioFind | Parkinson | 120 samples | Yes | No | |
| Cardiovascular | dbGaP | Framingham cohort study | >1,000 samples | Yes | No | |
| Animal data | Jacksons labs | Various | >1,000 models | No | Yes |
Last updated 8 April 2015