Home

ASCT+B Cell Types Data from Azimuth Reference Data With Summaries

Overview

ASCT+B tables represent cell by gene (CxG) relationships that are also captured in the HuBMAP Azimuth references. This site provides the cell type typology for all existing Azimuth annotated reference datasets; the Azimuth cell type typology trees can be visualized in the ASCT+B Reporter.

We also provide easy access to results for comparing CxG in ASCT+B vs. CxG in Azimuth. In Jan 2022, Azimuth supports single-cell RNA-seq data exclusively. As more experimental data becomes available and additional types of data are supported (e.g., proteins, lipids, metabolites), data differences will decrease.

Azimuth Cell Type Typologies and Counts

In Jan 2022, eight molecular reference maps for human are available via Azimuth. For each we provide the cell type typology as a file that can be visualized in the ASCT+B Reporter together with a table that lists the annotation level and the number of cell types for each unique cell in the organ-specific Azimuth reference, see Table 1.

Comparison of CxG in ASCT+B vs. Azimuth

Table 3 shows the comparison of the CxG matrix in ASCT+B tables vs. CxG matrix in Azimuth for each organ in Jan 2022. An automatically generated, up-to-date comparison is available here; this xls also contains separate sheets with cell types that are not (yet) covered in the ASCT+B tables. Details on how the comparison is calculated are on GitHub. Note that not all Azimuth cell types have CL IDs; in these cases, matching is done based on cell type names.

Data from https://github.com/satijalab/azimuth_website has been parsed to derive cell type typologies:

Cell Types Annotation Levels in Azimuth Reference Total Cell Count in Aziumuth Reference Biomarkers
Azimuth ASCT+B v1.0 Matches Azimuth ASCT+B Matches
Unique Names Unique IDs Unique Names Unique IDs Using IDs Using labels
Bone Marrow & Blood 72 32 46 16 5 N/A 3 35,355 352 199 87
Brain 187 10 127 N/A 123 N/A 4 24,402 864 254 152
Heart 24 N/A 17 18 N/A 6 2 656,509 216 48 25
Kidney 53 39 61 46 23 N/A 3 58,461 432 150 70
Lung 67 43 93 74 14 N/A 2 65,662 556 172 73
Pancreas 13 12 0 0 0 N/A 1 35,289 128 0 0
Spleen 49 N/A 66 N/A N/A 4 9 5,104 N/A N/A N/A
Lung v2 90 N/A 84 82 N/A 8 6 584,884 390 172 54

Code is available on GitHub.

Azimuth CT Counts

Data from https://github.com/satijalab/azimuth_website has been parsed to derive cell type counts:

Code is available on GitHub.

Code on Github

All code is freely available on GitHub.

Terms of Use

HuBMAP data are supplied with no warranties, expressed or implied, including without limitation, any warranty of merchantability or fitness for a particular purpose or non-infringement. No warranty with respect to the HuBMAP infrastructure is provided, including without limitation, any uptime warranty. The Parties make no representations that the use of the data will not infringe any patent or proprietary rights of third parties.

License

All CCF 3D reference objects are released under Attribution 4.0 International (CC BY 4.0).

Citation

If you use the data files v1.0 release, please cite this effort as follows:

Acknowledgements

This code and data was compiled by the HuBMAP MC-IU team in close collaboration with the MC-NYGC team.

References