Table 1.

High-content CRISPR screening systems.

Readout	Description	Model	System studied	Reference
Transcriptomic readout
Barcoded systems
Perturb-seq	gRNA-specific barcodes proximal to poly-A tail are recognized during scRNA-seq	Murine BMDCs, Human K562 cells in vitro	LPS stimulation response, Transcription factor functions, Cell fitness	(54)
		Human K562 cells in vitro	Unfolded protein response	(51)
CRISP-seq		Murine BMDCs in vitro and in vivo	Monocyte lineage differentiation and LPS-induced inflammatory response	(108)
Mosaic-seq		Human K562 cells in vitro	Enhancer target genes, Combinatorial enhancer activity	(109)
PoKI-seq	‘Pooled knockin sequencing’ Electroporation of RNP with a non-viral barcoded homology-directed repair template library coupled to scRNA-seq	Primary human T cells in vivo	Engineer and phenotype CAR T cells	(32)
ModPoKI-seq	‘Modular pooled knockin screening’ Modified PoKI-seq to reduce template switching	Primary human T cells in vitro and in vivo	Engineer and phenotype CAR T cells	(110)
Non-barcoded systems
CROP-seq	gRNA is proximal to poly-A tail for direct sequencing during scRNA-seq	Jurkat T cells in vitro	T cell receptor signaling	(19)
	CROP-seq paired with SLICE	Primary human T cells in vitro	T cell stimulation regulators	(16)
Direct-capture Perturb-seq	gRNA-specific primers bind to capture sequences in gRNA constant regions during scRNA-seq	Human K562 cells in vitro	Genetic interactions between cholesterol biosynthesis and DNA repair genes	(111)
		Human K562 cells, Human RPE1 cells in vitro	Mitochondrial stress response, ribosome biogenesis, integrator complex, erythroid and myeloid differentiation, and aneuploidy	(112)
		Murine TILs in vivo	Chromatin remodeling complexes in T cell exhaustion	(33)
CRISPRa Perturb-seq	Capture sequences in gRNA scaffold regions are recognized during scRNA-seq	Primary human T cells in vitro	Stimulation-response cytokine regulators	(113)
TAP-seq	‘Targeted Perturb-seq’ Gene-specific primers amplify transcripts of interest during CROP-seq	Human K562 cells in vitro	Enhancer-target gene pairs	(114)
Epigenetic readout
Perturb-ATAC	Pooled primers target flanking regions of barcode or gRNA during ATAC-seq; Micro-well fluidics platform	Human GM12878 lymphoblastic cells in vitro	Nucleosome structure alterations	(115)
CRISPR-sciATAC	gRNA and ATAC fragments are labeled with combinatorial barcodes for detection during ATAC-seq; CROP-seq vector; Micro-well-based	Human K562 cells in vitro	Chromatin accessibility	(116)
Spear-ATAC	Pre-integrated adaptors flank gRNA for direct amplification from genomic DNA during scATAC-seq; Droplet-based	Human K562 cells, GM12878 lymphoblastic cells, MCF7 breast cancer cells in vitro	Epigenetic alterations to transcription factor binding sites	(20)
Proteomic readout
ECCITE-seq	‘Expanded CRISPR-compatible CITE-seq’ gRNA scaffold-specific primers detect gRNA during scRNA-seq	Human K562 cells in vitro	Small sub-pool validation screen targeting known cell surface markers and intracellular signaling molecules	(117)
		THP-1 monocyte leukemia cells in vitro	Transcriptional and post-transcriptional regulators of PD-L1 expression	(118)
		Human cutaneous T-cell lymphoma samples in vitro	Malignancy of different T cell clonotypes, Characteristics of skin vs blood microenvironment	(119)
Perturb-CITE-seq	CROP-seq coupled with CITE-seq	Patient-derived melanoma cells in vitro	Mechanisms of ICI resistance	(21)
‘Pro-code’ CYTOF	Protein-encoding barcodes (Pro-Codes) couple CRISPR screens with mass cytometry	Breast cancer 4T1 cells in vitro	Regulators of breast cancer immune evasion	(120)
Optical readout
Feldman et al.	Barcoded or non-barcoded CRISPR screens coupled with imaging	HeLa cells in vitro	Regulators of NF-kB signaling	(121)
Perturb-map	Protein-encoding barcodes (Pro-Codes) couple CRISPR screens with imaging and transcriptomics	Lung adenocarcinoma cells in vivo	Regulators of TME	(22)