Question: How to decide if the 5’ CRISPR assay or the 3’ CRISPR assay best fit my experiment?
Answer: Sensitivity is comparable between the 3’ and 5’ CRISPR screening assays, both in terms of gene expression and guide capture.
The Single Cell 3' CRISPR Screening is enabled by engineering sgRNAs with one of two possible capture sequences that are required for assay compatibility. The Single Cell 5' CRISPR Screening approach is compatible with most Cas9 CRISPR vectors and does not require integration of specific capture sequences into the sgRNAs for compatibility.
In the majority of cases, customers should consider the 5’ CRISPR assay. The following criteria can help you decide which assay best fits your experiment.
Customers should select the 5’ CRISPR assay if they meet the following criteria:
- They already have a pre-built, compatible guide RNA library they want to use in the single cell CRISPR screening workflow.
- They are new to single cell CRISPR screening.
- They are experienced with single cell CRISPR screening, but do not wish to perform additional steps to modify guide libraries with assay-specific sequences.
Customers should select the 3’ CRISPR assay if they meet the following criteria:
- They want to compare their single cell CRISPR experiment to data from previous experiments that also used the 3’ assay. The same CRISPR assay should be used in order to minimize batch effects.
- They perform pilot experiments to determine the optimal choice of capture sequence and integration site for their cell type, as outlined in this article.
More information can be found in this blog.
Products: Single Cell Gene Expression, Single Cell Immune Profiling