How can I extract the sequences of guide RNAs (gRNAs) targeting a specific gene from the DepMap portal?

27 January 2025 1 5K Report

Dear All,

I am new to working with the DepMap database and would appreciate your guidance. I understand that DepMap includes a collection of genes tested for knockdown using CRISPR/RNAi methodologies. However, I am unsure how to locate the sequences of the guide RNAs (gRNAs) used in these experiments.

If anyone could provide instructions or point me toward relevant resources, I would be very grateful.

Thank you for your help.

Best regards,

Amit

Amit Kumar

I am able to download CRISPRinferredguideefficicay excel file from Depmap portal. But it has only guide RNA sequence and their respective efficacies and No gene annotation. How to find out which sequence is which gene. There are 1900000 sequences therefore manual blast is not feasible.

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