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