Dataset Information

Single Genetic Perturbation Data

Schematic of the genetic perturbation dataset used in this paper.

Specifications for single genetic perturbation dataset

Alias ID	Sample Type	CRISPR Type	Perturbation Type	Perturbation Count	Number of Control cells	Gene Count	Total Number of Cells	Acquisition Method	Accession ID
Replogle22_a	RPE1 cells	CRISPRi	Single	654	10000	2535	137927	scPerturb	7041849 (Zenodo)
Replogle22_b	K562 cells	CRISPRi	Single	1000	10000	2797	221295	scPerturb	7041849 (Zenodo)
Nadig25_a	Jurkat cells	CRISPRi	Single	788	10000	2597	152211	scPerturb	13350497 (Zenodo)
Nadig25_b	HepG2 cells	CRISPRi	Single	225	4976	2999	44091	scPerturb	13350497 (Zenodo)
Norman19	Lymphoblasts	CRISPRa	Single	102	10000	1834	66391	Direct download from Biohub	7041849 (Zenodo)
Marson_a	CD4+ T-cells	CRISPRi	Single	966	10000	3166	323529	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_b	CD4+ T-cells	CRISPRi	Single	970	10000	4645	284722	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_c	CD4+ T-cells	CRISPRi	Single	968	10000	4688	261396	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_d	CD4+ T-cells	CRISPRi	Single	977	10000	4449	457477	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_e	CD4+ T-cells	CRISPRi	Single	978	10000	3576	462770	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_f	CD4+ T-cells	CRISPRi	Single	961	10000	3490	407131	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_g	CD4+ T-cells	CRISPRi	Single	959	10000	4828	339227	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_h	CD4+ T-cells	CRISPRi	Single	964	10000	4311	388729	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_i	CD4+ T-cells	CRISPRi	Single	972	10000	4054	234451	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_j	CD4+ T-cells	CRISPRi	Single	972	10000	3493	407674	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Marson_k	CD4+ T-cells	CRISPRi	Single	969	10000	4605	284487	Direct download from Biohub	SRP643211 (SRA) / GSE314342 (GEO)
Frangieh21	Melanocytes	CRISPRi	Single	219	10000	2143	160661	scPerturb	7041849 (Zenodo)
Tian19_a	iPSC-induced neurons	CRISPRi	Single	26	10000	92	79704	scPerturb	7041849 (Zenodo)
Tian19_b	iPSC cells	CRISPRi	Single	26	10000	39	139642	scPerturb	7041849 (Zenodo)
Tian21_a	iPSC-induced neurons	CRISPRi	Single	172	437	2912	30910	scPerturb	7041849 (Zenodo)
Tian21_b	iPSC-induced neurons	CRISPRi	Single	91	434	1979	20230	scPerturb	7041849 (Zenodo)
Binan25	Astrocytes	CRISPRi	Single	54	9633	211	4926	Direct download	GSE221321 (GEO)
XAtlas25_a	HCT116 cells	CRISPRi	Single	996	10000	4168	375749	Direct download	29190726 (Figshare)
XAtlas25_b	HEK293 T-cells	CRISPRi	Single	994	10000	5613	501023	Direct download	29190726 (Figshare)
Akana26	Melanoma cells	CIRSPRa	Single	57	2660	4273	19722	Direct download	15213596 (Zenodo)
Kaden25_a	PRE1 cells	CIRSPRa	Single	1000	10000	2231	110000	Direct download	15213597 (Zenodo)
Kaden25_b	Fibroblast cells	CIRSPRa	Single	1000	10000	2878	110000	Direct download	15213597 (Zenodo)
Schmidt22	T-cells	CIRSPRa	Single	69	3274	1241	57817	Direct download	5784651 (Zenodo)

Double Genetic Perturbation Data

Specifications for double genetic perturbation dataset

Alias ID	Sample Type	CRISPR Type	Perturbation Type	Perturbation Count	Number of Control cells	Gene Count	Total Number of Cells	Acquisition Method	Accession ID
Norman_19	lymphoblasts	CRISPRa	double	126	11855	1000	52223	scPerturb	7041849 (Zenodo)
Tian19_a	iPSC-induced neurons	CRISPRi	double	322	15580	1000	42365	scPerturb	7041849 (Zenodo)
Tian19_b	iPSC cells	CRISPRi	double	322	1000	57350	57350	scPerturb	7041849 (Zenodo)
Proper_filtered	K562 cells	CRISPRa	double	104	2280	1000	29970	Direct Download	SUB15796302 (SRA)

Drug Perturbation Data

For drug perturbations, we used sci-Plex and Tahoe-100M.