Assays

Term Category	Assay	Preferred Assay Title	cell line	differentiated cell specimen	gastruloid	organoid	primary cell	reprogrammed cell specimen	tissue	Grand Total
CRISPR screens	in vitro CRISPR screen using flow cytometry	CRISPR FlowFISH screen	835							835
		Variant-EFFECTS	491							491
		CRISPR FACS screen	64				70			134
	cas mediated mutagenesis	SGE	1.0K							1.0K
	in vitro CRISPR screen using single-cell RNA-seq	Perturb-seq	58	173			9			240
		TAP-seq	31							31
		scCRISPR screen	4	4						8
	in vitro CRISPR screen assay	Proliferation CRISPR screen	45							45
		CRISPR MACS screen	9							9
		Migration CRISPR screen	6							6
		Parse SPLiT-seq	2							2
CRISPR screens Total			2.6K	177			79			2.8K
gene expression	single-nucleus RNA sequencing assay	10x multiome		8		47	81	13	644	793
		Parse SPLiT-seq							296	296
		10x multiome with MULTI-seq	31	48	4				11	94
		SHARE-seq							2	2
	single-cell RNA sequencing assay	SHARE-seq	19	95		35	209		57	415
		10x multiome with scMito-seq					38			38
		scRNA-seq	18	10			3			31
		Parse SPLiT-seq					2			2
	bulk RNA-seq assay	RNA-seq	33	48			36			117
	single cell nascent transcription sequencing	scNT-seq2		79						79
	single cell nascent transcription sequencing	scNT-seq		4						4
	direct RNA sequencing assay	ONT dRNA							8	8
gene expression Total			101	292	4	82	369	13	1.0K	1.9K
chromatin accessibility	single-nucleus ATAC-seq	10x multiome		8		47	81	13	644	793
		10x multiome with MULTI-seq	31	48	4				11	94
		SHARE-seq							2	2
		scATAC-seq		1			1			2
	single-cell ATAC-seq	SHARE-seq	24	120		35	205		52	436
		10x multiome with scMito-seq					38			38
		10x multiome	17							17
		scATAC-seq		4			1			5
	bulk assay for transposase-accessible chromatin using sequencing	ATAC-seq	13	24			26			63
chromatin accessibility Total			85	205	4	82	352	13	709	1.4K
protein	flow cytometry assay	VAMP-seq (MultiSTEP)	144							144
protein	flow cytometry assay	VAMP-seq	40							40
protein Total			184							184
multiome	single nucleus methylation and chromatin conformation capture sequencing	snM3C-seq				42	4	32		78
multiome	single-nucleus methylcytosine and transcriptome sequencing assay	snMCT-seq					8	42		50
multiome Total						42	12	74		128
reporter	massively parallel reporter assay	MPRA	10	38						48
		lentiMPRA	12	15						27
		electroporated MPRA	11							11
	self-transcribing active regulatory region sequencing assay	SUPERSTARR	16							16
reporter Total			49	53						102
3D chromatin structure	Hi-C assay	HiCAR	6	14						20
3D chromatin structure	Hi-C assay	Hi-C	3	9						12
3D chromatin structure Total			9	23						32
DNA binding	transcription factor binding site identification by ChIP-Seq assay	TF ChIP-seq	2	14						16
DNA binding	histone modification identification by ChIP-Seq assay	Histone ChIP-seq	2	6						8
DNA binding Total			4	20						24
genetic profiling	whole genome sequencing assay	WGS					23			23
genetic profiling Total							23			23
no category	spatial transcriptomics	Spatial transcriptomics							8	8
no category	single cell massively parallel reporter assay	MPRA (scQer)		6						6
no category Total				6					8	14
DNA methylation	m6A-MTase sequencing assay	ONT Fiber-seq							8	8
DNA methylation Total									8	8