On the design of CRISPR-based single-cell molecular screens.
Andrew J HillJosé L McFaline-FigueroaLea M StaritaMolly J GasperiniKenneth A MatreyekJonathan PackerDana JacksonJay ShendureCole TrapnellPublished in: Nature methods (2018)
Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
Keyphrases
- genome wide
- rna seq
- single cell
- high throughput
- dna methylation
- induced apoptosis
- copy number
- genome editing
- cell cycle arrest
- crispr cas
- climate change
- nucleic acid
- cell death
- endoplasmic reticulum stress
- gene expression
- molecularly imprinted
- randomized controlled trial
- gene therapy
- single molecule
- mass spectrometry
- phase iii
- meta analyses