Can I identify a cell type by comparison with published transcriptomes of known cell types?

Question

[jody-summers]

We have isolated a cell type by FACS and want to identify/characterize these cells using RNA seq and transcriptome analyses. I am trying to find a method by which we can compare our transcriptome with published transcriptomes of known cell types (of the same or different species) to at least have some idea of the cell type that we are working with. I have found the Sincera resource, but it seems that one needs extensive experience with scripting and working with the R program. I was hoping for something like "whole transcriptome blast analyses"... that would come back with a probability of the similarity of our transcriptome with other ones. This is my first RNA seq experiment and I would appreciate any information on how to approach this project.

Answer 1

[philippe.mcqt]

Sincera seems like what you are looking for. I don't know of any 'ready to blast' tools that would allow to identify cell type. I think it might depends on what you are looking for, do you know what cell type you might have from the FACS analysis ? If so it is always possible to download similar experiment from ArrayExpress, extract signatures genes and compare to your own experiment signatures genes.

Answer 2

[TriS]

I don't think there is a "one click" analysis that you can do to get what you want. there are however examples of signatures that are more characteristic of some cell populations i.e. there are signature for breast or prostate cancer.

another thing I can think about is the ESTIMATE approach, they do have a web app for TCGA data but I fear you will still have to know some coding to run it on your data.

I feel that you don't have much coding experience, which is totally fine (i.e I don't know how to run FACS!), so I'd suggest you to partner up with a bioinformatician in your institution to play with your data