How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)?
1
0
Entering edit mode
3.0 years ago
mrj ▴ 180

I have a list of conserved cell type markers discovered from Seurat. I would like to annotate clusters with cell types based on that.

For example, here is a profile of cell type markers (from mouse genome) I am dealing with

Gm42418
Nme2
Rpl19
Malat1
AY036118
mt-Co3
mt-Nd2
Ahnak
Hnrnpu
mt-Atp6
mt-Atp8
mt-Nd5
Ly6g
Hist1h4d
Nedd4
mt-Nd1
Lars2
Xist
Prrc2c
Myof
mt-Nd4l
mt-Nd6
mt-Nd3
mt-Co1
Prpf4b
Hist1h1e
mt-Cytb
mt-Co2
mt-Nd4
Hist1h1b
Gm26917

how can I computationally predict the cell type if the genome is mouse mm10?

Seurat scRNA-seq cell_type conserved_cell_type_markers • 1.9k views
ADD COMMENT
1
Entering edit mode
3.0 years ago
Refine ▴ 20

Hi ! I'm sorry I'm not good at English. I am not able to answer your question because I do not know how to automatically judge cell types, but I noticed some things in your result.

In my experience, Gm42418 and AY036118 genes are detected in noisy cluster for me, and I sometimes can not identify cell types. Similarly, "mt-"genes are also detected in noisy cluster and these genes are markers of dead cells. You might be confused by these factors ( and I do not know why they occur).

Parhaps they might be improved by some changes as follows.

  1. Check whether nFeature_RNA & percent.mt are appriximately same as other clusters.
  2. Use SCT method and regress percent.mt.(DE is by RNA assay.)

If possible, please show me your code ? I might be able to advise you a little more.

ADD COMMENT
1
Entering edit mode

Thank you so much for your insight. It made me go back to my code and realize that I have not limited the presence of mitochondrial contaminated cells.

ADD REPLY
1
Entering edit mode

I am happy to hear that !

ADD REPLY

Login before adding your answer.

Traffic: 1452 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6