Question: Marker genes for different cell types
1
gravatar for halo22
2.6 years ago by
halo22140
Indianapolis, IN
halo22140 wrote:

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.

rna-seq rna singlecell • 2.4k views
ADD COMMENTlink modified 2 days ago by jrleary60 • written 2.6 years ago by halo22140

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster43k

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

ADD REPLYlink written 2.6 years ago by halo22140
0
gravatar for Jean-Karim Heriche
2.6 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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

ADD COMMENTlink written 2.6 years ago by Jean-Karim Heriche21k
0
gravatar for EagleEye
2.6 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

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

ADD COMMENTlink written 2.6 years ago by EagleEye6.6k
0
gravatar for jrleary
2 days ago by
jrleary60
Lineberger Comprehensive Cancer Center
jrleary60 wrote:

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.

ADD COMMENTlink written 2 days ago by jrleary60
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