Marker genes for different cell types

Question

[halo22]

Hello All,

This may sound like a vague question but your help and inputs on this could really help me move forward. I am helping a bench scientist with his single cell RNA sequencing data generated using drop-seq platform. I did the basic QC analysis and everything seems to be fine with that. Then I performed clustering to find genes with similar expression profile, I did that by using seurat(http://satijalab.org/seurat/pbmc-tutorial.html). I'm almost done with the analysis and my t-SNE plot shows me 5 decent clusters. I guess at the end I would have to label each cluster by a cell type provided that a particular cell-type is known to express a marker-gene which might be a part of a cluster. Is there a universal list of cell-type gene marker that is available and could be applied with what I am doing? Please let me know if the question makes sense, I am trying to do something like the "Assigning cell type identity to clusters" section of the seurat tutorial(http://satijalab.org/seurat/pbmc-tutorial.html).

Update: Memory cells CCR7+/CD45RA- were used in the experiment and were extracted from blood.

[WouterDeCoster]

Are you working on a specific tissue? Might be worth mentioning.

[halo22]

Thank you for your response. I have updated my post.

Answer 1

[jrleary]

In my opinion annotating cell clusters using marker genes by hand is a massive pain and is very subjective. I used the SingleR package, which iteratively compares non-parametric gene expression profile correlations of your cells with annotated reference cells. It's very easy to set up and use and I've gotten pretty reliable results using it.

Answer 2

[Jean-Karim Heriche]

There's a list of CD (cluster of differentiation) antigens and the cells that express them here.

Answer 3

[EagleEye]

This might be an alternative and interesting to you for predicting marker genes from your dataset,

http://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/my-vignette.html