How many gRNAs from a GeCKO screen for a gene to be truly significant

I've just run through my first GeCKO screen and the bioinformatician has given me a list of genes which seem to be significant. For none of these genes are more than 3 of the sgRNA's found to be significant (I did the full library A and B screen so have 6 guides for each gene). One of the genes only has one sgRNA coming up as significant. I was just wondering in terms of results what people take as truly significant?

Also with my treatment which proved more strong than I had anticipated I had less than the ideal number of cells at the end of the experiment for library generation (control untreated group had the right number of cells). How much would this effect the results analysis?

I'll obviously be repeating the screen with the same conditions and putting more cells through the treatment this time but it would be good to get some thoughts on results output.

any feedback much appreciated


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Fuchsia Kelpieabout 4 years ago

Usually I would expect to see the majority of sgRNAs to be significantly enriched for a significant gene, but this depends on how you did your analysis and your screen's signal-to-noise ratio. The way I typically look at these lists of genes is I see them as a ranked list and not whether they are significant based on statistical analyses because each screen is unique. Then I will validate the top 5-10 genes by re-introducing the sgRNAs individually and measuring the screening phenotype. That would be the

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