How to find common essential genes for CNS

Q&A
1

Hi, I am running genome wide crispr on CNS cell lines and need to define common essential genes as a positive gRNA depletion control. How do I get the list of common essential genes?

Also are common essential are define as genes that is essential across all cell lines, does not matter which tissue there are from, or narrowing it down to specific tissue is important because genes behave differently across different tissues?

In shinnyDepMap website https://labsyspharm.shinyapps.io/depmap/
I am able to see the score of gene essentiality, however, is there a way to bunch up a bunch of gene sets that have high dependency score?

Please help.
Thank you.

2

Hi Hikarue,

You can download the DepMap-identified common essential genes from the file CRISPRInferredCommonEssentials. This is genes that are essential across all tissues. This is a good set of positive controls. It is up to you whether genes that are specifically essential in all CNS cell lines are of interest to you, but that list is a good set of positive controls for screens in any tissue.