What is the Human Cell Atlas project
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The Human Cell Atlas (HCA) project is international endeavour to create comprehensive reference maps of all cells in the human body. This collection of molecular single-cell maps will provide enormous insight into cellular biology, as well as providing a reference database from which automated cellular classification can be achieved. These efforts are partnered by other atlas-level projects, including the LifeTime initiative and the NIH Human BioMolecular Atlas Program (HubMAP) consortium. |
Multi-modal single-cell technologies
Much of the data generated for the various single-cell and inflammatory atlas projects are generated using single-cell RNA sequencing (scRNAseq). In increasing frequency, datasets are being generated by incorporating multi-modal technologies, such as CITE-seq, where transcripts and antibodies on single-cells can be measured simultaneously. The presence of antibody labelling in these atlas datasets allows for direct integration between single-cell atlas datasets and independent high-dimensional cytometry datasets. An example of thise approach is described in Hao 2020, where CyTOF and CITE-seq data was integrated together using tools such as Azimuth.
Interfacing with atlas datasets using Spectre
Challenges
- Different challenges and requirements in analysis
- Large cell volumes
- Differences in QC and pre-processing
- Differences in # of features, and implications for integration etc
Our approaches
- Interface with data portals, or download data and do it manually…
- Find common features
- Re-render the resolvable populations in the reference dataset
- Perform alignment
- Perform label transfer
Further cell atlas resources and guidelines
In addition to direct interactions
seeking to help define the contribution of high-dimensional cytometry and imaging technologies to the HCA objectives (Czechowska et al. 2018, WS06: ‘Cytometry in the Era of the Human Cell Atlas’).