What's the difference between Achilles_gene_effect.csv and CRISPR_gene_effect.csv?

Q&A
1

Hi. I’m wondering the difference between Achilles_gene_effect.csv and CRISPR_gene_effect.csv. Does CRISPR_gene_effect.csv integrate the data from Achilles_gene_effect.csv?
If I want to download the a CRISPR genetic screening dataset, the appropriate dataset would be the CRISPR (DepMap 22Q1 Public+Score, Chronos), the CRISPR_gene_effect.csv, or the Achilles_gene_effect.csv?
For RNAi screening dataset, is the RNAi (Achilles+DRIVE+Marcotte, DEMETER2) recommended?
Thanks.

2

Yes, I’d generally recommend for most usage the “RNAi (Achilles+DRIVE+Marcotte, DEMETER2)” dataset for looking at RNAi effects.

As far as Achilles_gene_effect.csv and CRISPR_gene_effect.csv:

Achilles_gene_effect is data generated at the Broad, whereas CRISPR_gene_effect is a dataset which integrates data from Project Score at Sanger with the data from the Broad.

If you want the dataset with the most samples and our best summary of gene effects from knocking out genes, then yes, I’d recommend “CRISPR (DepMap 22Q1 Public+Score, Chronos)” which is the “CRISPR_gene_effect.csv” file.

(It’s perhaps worth noting that some genes screened by Achilles are not represented in the Score dataset and are therefore dropped in the combined dataset. So if a gene you are interested in isn’t present in the combined dataset, you may want to check just Achilles_gene_effect.csv)

Thanks,
Phil

3

Hi Phil,

If “Achilles_gene_effect.csv” is the Depmap broad data and “CRISPR_gene_effect.csv” is a combined dataset. What is CRISPR (Project Score, CERES) associated csv “gene_effect.csv” is this Sanger Project score data only?

If it is, I can see that my gene of interest is included in the CRISPR (Project Score, CERES) dataset from the DepMap website however when I search for my gene of interest on the https://score.depmap.sanger.ac.uk/ it is not found.

Can you help me in finding the reason for this inconsistency?

Best wishes,
Nathan