Question: Gene list of Neuronal Markers for TSNE plot
0
gravatar for DNA_001
5 weeks 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 • 163 views
ADD COMMENTlink modified 5 weeks ago by Friederike3.3k • written 5 weeks ago by DNA_0010
1
gravatar for nancy
5 weeks ago by
nancy70
nancy70 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 5 weeks ago by nancy70

Thanks! This is very interesting :)

ADD REPLYlink written 5 weeks ago by DNA_0010
1
gravatar for Friederike
5 weeks ago by
Friederike3.3k
United States
Friederike3.3k 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 5 weeks ago by Friederike3.3k

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

ADD REPLYlink written 5 weeks ago by DNA_0010
0
gravatar for geek_y
5 weeks ago by
geek_y9.3k
Barcelona/CRG/London/Imperial
geek_y9.3k 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 5 weeks ago • written 5 weeks ago by geek_y9.3k
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