Is There a Website for Finding Detailed Information for Different Cell Lines?
Yes, several specialized websites provide detailed information on various cell lines, including gene expression, mutations, and other molecular data. Notable resources are DepMap Portal, Cellosaurus, ENCODE, Harmonizome, GEO, and cancer-focused databases like CCLE.
Key Websites for Cell Line Data
- DepMap Portal offers extensive datasets on around 1,000 cancer cell lines. It includes gene expression, mutations, and copy number variations, making it ideal for cancer research. Visit depmap.org for details.
- Cellosaurus, part of the Expasy bioinformatics platform, is a comprehensive database for detailed information on individual cell lines. It contains data on cell line characteristics and links to mutation information. See Cellosaurus.
- ENCODE Project provides raw and processed data for many human and mouse cell lines. It is suited for large-scale genomic studies. Access their data via the ENCODE portal.
- Harmonizome supplies lists of highly and lowly expressed genes for specific cell lines like HEK293T and Jurkat, among others. The database is accessible at Harmonizome.
- Gene Expression Omnibus (GEO) is a useful source for gene expression data, especially when expression is context-dependent. GEO archives datasets from various experiments and conditions.
- Cancer Cell Line Encyclopedia (CCLE) provides extensive molecular profiling of cancer cell lines, overlapping somewhat with DepMap but distinct in scope.
Additional Resources and Tips
The American Type Culture Collection (ATCC) offers a broad catalog of cell lines but may lack detailed molecular data like gene expression profiles. Researchers often consult study-specific supplementary data or the Sequence Read Archive (SRA) for mutation and expression data from published sequencing projects focused on their cell lines of interest.
When direct datasets are unavailable, contacting authors of relevant studies can yield mutation calls or filtered data, especially for specialized or less common cell lines.
Summary of Resources
| Resource | Focus | Data Types | Website |
|---|---|---|---|
| DepMap | Cancer Cell Lines | Expression, Mutations, Copy Number | depmap.org |
| Cellosaurus | All Cell Lines | Info, Mutations Links | web.expasy.org/cellosaurus |
| ENCODE | Human/Mouse Cell Lines | Raw and Processed Genomic Data | encodeproject.org |
| Harmonizome | Selected Cell Lines | Gene Expression Profiles | maayanlab.cloud/Harmonizome |
| GEO | Various Cell Lines | Gene Expression Data | ncbi.nlm.nih.gov/geo |
| CCLE | Cancer Cell Lines | Molecular Profiling | portals.broadinstitute.org/ccle |
Key Takeaways
- DepMap and CCLE specialize in cancer cell line molecular data.
- Cellosaurus offers detailed general cell line information and links to mutation data.
- ENCODE and GEO provide abundant genomic and expression datasets for human and mouse lines.
- Harmonizome lists gene expression patterns for select cell lines.
- ATCC catalogs cell lines but may lack detailed expression data.
- Supplementary data from published studies and SRA remain valuable for context-specific queries.
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