Question: Is there a comprehensive gene list available that will enable me to annotate clusters to their respective cell types?
Answer: 10x Genomics does not provide official guidelines on annotating cell types. However, the information below might help.
For PBMCs, you could use the 10 marker genes listed in the AMLBloodCell.csv. That is used in our tutorial on annotating cell types using Loupe Browser.
You could also use the third-party articles/resources listed below. Please note that this is not a comprehensive list. Cell type annotation is an active area of research, and you may find more updated information based on your search.
- Seurat's find.markers() function
- Human Cell Atlas Data Portal
- CellMarker: a manually curated resource of cell markers in human and mouse
- Identifying cell populations with scRNASeq
- CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing
- Tabula Muris: a compendium of single-cell transcriptome data from mice
- Tabula Sapiens: a growing repository of detailed gene expression profile in human tissues
Please contact the respective authors of each article/tool for more information.
Disclaimer: This article and code-snippet are provided for instructional purposes only. 10x Genomics does not support or guarantee the listed tools or code.