Gene list of Neuronal Markers for TSNE plot

Question

[DNA_001]

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!! :)

Answer 1

[Friederike]

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.

[DNA_001]

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

[Friederike]

updating my answer to point out that by now there are a couple of packages that will support you with the automated annotation of scRNA-seq data, e.g. SingleR. It comes with a set of reference data, including the Human Primary Cell Atlas that does cover a couple of neuronal markers. That being said, it's probably a good idea to download another scRNA-seq data set that has similar cell types to the ones you are expecting and use that as a reference; that is also fairly straight-forwardly done with SingleR.

Answer 2

[nancy]

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

[paria]

Hello, I was trying to open the link. But access is forbidden. I was wondering how I can have access to this link? Thanks

[DNA_001]

Thanks! This is very interesting :)

Answer 3

[GouthamAtla]

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