Question: Gene list of Neuronal Markers for TSNE plot
0
gravatar for DNA_001
13 months ago by
DNA_0010
DNA_0010 wrote:

Dear All,

I want to create a TSNE plot for RNAseq data (brain tumours) and I need to use a list of neuronal markers- to check which clusters have which type of cells.

I am creating my own excel sheet at the moment by searching literature, which is getting tough at the moment since there are so many. I was wondering if there a simpler way somehow to get list of genes enriched in the brain (example: markers for Astrocytes, glial cells, neurons..etc)

I would be very happy if someone could help me with such a list or have any advice to make this faster.

Thank you very much in advance!! :)

gene • 544 views
ADD COMMENTlink modified 13 months ago by Friederike5.4k • written 13 months ago by DNA_0010
1
gravatar for nancy
13 months ago by
nancy80
nancy80 wrote:

Ben Barres lab has made some data publicly available (can dowload an excel spreadsheet with fpkms) here, as well as look up genes enriched in each cell type.

https://web.stanford.edu/group/barres_lab/brain_rnaseq.html

ADD COMMENTlink written 13 months ago by nancy80

Thanks! This is very interesting :)

ADD REPLYlink written 13 months ago by DNA_0010
1
gravatar for Friederike
13 months ago by
Friederike5.4k
United States
Friederike5.4k wrote:

Welcome to the cumbersome and surprisingly ambiguous world of "identifying cell types" from scRNA-seq data!

Both of the answers are helpful, the first thing that came to my mind was The Allen Brain Atlas -- but the more you ask, the more markers you'll get, similar to what probably happened when you started looking at the literature. My advice is to look for markers that are very (!) strongly expressed (not transcription factors!), those will give you the most robust indications; and if you're lucky, you may not need more than 4-5 per cell type if the clustering is very clear-cut.

ADD COMMENTlink written 13 months ago by Friederike5.4k

Thanks! Yes, the list is a non-exhausting one! But this helps! :)

ADD REPLYlink written 13 months ago by DNA_0010
0
gravatar for geek_y
13 months ago by
geek_y10k
Barcelona
geek_y10k wrote:

You should look at single Cell RNA-Seq papers on brain to get cell-type specific markers. For example, there is a review

ADD COMMENTlink modified 13 months ago • written 13 months ago by geek_y10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1093 users visited in the last hour