Table 1.

Protein acceleration datasets and parameters

Dataset	CITE-seq	REAP-seq	ECCITE-seq ctrl	ECCITE-seq CTCL	10X 1k	10X 10k
RNA data	GSM2695381	GSM2685238	GSM3596095	GSM3596100	See Methods	See Methods
Protein data	GSM2695382	GSM2685243	GSM3596096	GSM3596101	See Methods	See Methods
Alignment software	Cell Ranger 2.2	Cell Ranger 1.3	Cell Ranger 3.0	Cell Ranger 3.0	kallisto 0.46	kallisto 0.46
Counting software	velocyto 0.17	velocyto 0.17	velocyto 0.17	velocyto 0.17	kallisto 0.46	kallisto 0.46
Reference genome	GRCh38	hg19	hg19	hg19	GRCh38	GRCh38
Cell count	1780	3158	5084	5317	709	7855
Velocity genes	1172	1338	591	667	1114	920
Antibodies	10	41	49	49	17	17
Velocity proteins	7	16	11	12	7	8
Cell types found	5	4	4	3	5	5
Imputation k	400	800	800	800	50	50
Clustering method	MVP	RVP	RVP	MVP	MVP	MVP
Embedding	PC2/3 and t-SNE	t-SNE	t-SNE	t-SNE	t-SNE	t-SNE

MVP ModularityVertexPartition, RVP RBERVertexPartition, PCA principal component, t-SNE t-Stochastic Neighbor Embedding