About the Data
We are committed to making Gray BRCA Atlas data available to the scientific community. Here you will find information describing the various Gray BRCA Pre-Cancer Atlas data types and how they are collected, analyzed, and shared.
Data Types
The Gray BRCA Precancer Atlas is currently comprised of the following data types:
| Assay | Data Type | Atlas | Data Access | Visualization Tools |
|---|---|---|---|---|
| High depth targeted DNA sequencing | DNA Sequencing | Breast | EGA and AWS1 | TBD |
| Single Cell RNA Sequencing 10X 3’ | Single Cell RNA Sequencing | Breast | GEO2 | TBD |
| FLEX Single Cell RNA Sequencing 10X | Single Cell Sequencing | Breast | GEO | Broad Single Cell Portal3 |
| ATAC Sequencing | Single Cell Sequencing | Breast | GEO | Broad Single Cell Portal, UCSC Cell Browser4 |
| DLP+ scWGS | Sequencing | Breast | EGA, AWS | TBD |
| GeoMx micro-region transcript profiling | Spatial RNA | Ovarian | GEO | cBioPortal6 |
| CODEX | Imaging | Breast | AWS | Minerva7 |
| Cyclic Immunofluorescence (CyCIF) imaging | Whole-Slide Multiplexed Imaging | Breast, Ovarian | AWS | Minerva, cBioPortal |
| Hematoxylin and Eosin (H&E) images | Whole-Slide Imaging | Breast, Ovarian | AWS | Minerva |
| Orion | Whole-Slide Multiplexed Imaging | Breast, Ovarian | AWS | Minerva |
| Orion-FISH | Spatial DNA | Breast, Ovarian | AWS | Minerva, cBioPortal |
| Xenium | Image-based Spatial Transcriptomics | Ovarian | TBD | TBD |
Public Data Access
A key goal of the Gray BRCA Precancer Atlas is to provide access to primary data consistent with FAIR Principles. Data types with an available public repositories (i.e., transcriptomic data via GEO) are made available at the time of publication. Data without a clear subject repository are available in an AWS S3 bucket. AWS S3 access instructions will be shared when data is available to access. Email tissue-atlas(at)hms.harvard.edu if you have questions or experience issues.
Data Access References
1 AWS: http://aws.amazon.com/. Data access instructions available via Zenodo
2 GEO: https://www.ncbi.nlm.nih.gov/geo/
3 Broad Single Cell Portal: https://singlecell.broadinstitute.org/single_cell
4 UCSC Browser: https://cells.ucsc.edu/
5 European Genome-Phenome Archive (EGA): https://ega-archive.org/
6 cBioPortal: cbioportal.org
7 Minerva: Image data can be explored on this website at graybrcaatlas.org/image-data-explorations. Learn more about Minerva at minerva.im