Ideas to identify unique genes of each brain regions

Question

[Davy]

Hi all, I'm interested in studying the brain and its transcriptomics. Specifically, I would like to ask if anyone here knows the best way to determine whether a brain region has unique genetic markers.

Currently, I download datasets online and run cellranger and R Seurat pipelines to analyze the data.

Let's say I'm interested in studying the hippocampus CA1 region in the brain. The only method I can think of is to download its dataset and use the findMarkers() command with every other brain regions (as I believe this command only takes two parameters).

I feel this method is too tedious and biased. Can anyone suggest better methods or alternatives that I can use?

Any help is welcome!

Answer 1

[Kevin Blighe]

I would like to ask if anyone here knows the best way to determine whether a brain region has unique genetic markers.

.

Let's say I'm interested in studying the hippocampus CA1 region in the brain. The only method I can think of is to download its dataset and use the findMarkers() command

These 2 statements contradict each other. You want to find unique genetic markers, but then imply that you have only retrieved single-cell RNA seq data (scRNA-seq) data.

You could commence by just using the scRNA-seq data to find genes that are uniquely expressed in the hippocampus CA1 region compared to other brain tissue, and then do further research after that. Indeed, the findMarkers() function has limits - please employ your own custom methods.

It is literally impossible to answer your question in just one answer...

Good luck.

[Davy]

Thank you very much for your reply.

Let's say I'm interested in studying the hippocampus CA1 region in the brain. The only method I can think of is to download its dataset and use the findMarkers() command

Also apologies for the confusion of the above statement. What i meant about this statement is to download CA1 dataset, as well as datasets of other brain region, and compare them using the FindAllMarkers() command.

I wonder if there are alternatives that allow me to use the CA1 data to compare to all datasets simultaneously.

Thank you!