Table 1 Description of the 23 datasets used in the experiments.

Application	Dataset	Cell number	Class number	Protocal	Reference	Minor cell type (<5% total cell number)	Cell number of the smallest cell type
	Deng	268	6	Smart-seq2	Deng et al.⁴⁹	2	12
	Darmanis	466	9	SMARTer	Darmanis et al.⁵⁰	3	16
	Usoskin	622	4	STRT-Seq	Usoskin et al.⁵¹	0	81
	CampLiver	777	7	SMARTer	Camp et al.⁵²	0	70
	Baron Mouse	1886	13	inDrop	Baron et al.⁵³	8	6
Intra-datast Benchmark	Muraro	2122	9	CEL-Seq2	Muraro et al.⁵⁴	4	3
	Lake	3042	16	Fluidigm C1	Lake et al.⁵⁵	10	45
	Baron Human	8569	14	inDrop	Baron et al.⁵³	9	7
	Campbell	21,086	32	Drop-Seq	Campbell et al.⁵⁶	29	30
	Zilionis	34,558	9	inDrop	Zilionis et al.⁵⁷	4	108
	TM (Tabula Muris)	54,865	55	10X Genomics	Schaum et al.⁵⁸	48	24
	Zheng 68 K	65,943	11	10X Genomics	Zheng et al.⁵⁹	6	92
	PbmcBench 10X (V2)	23,154	9	10X Genomics (v2)	Ding et al.⁶⁰	4	132
	PbmcBench 10X (V3)	19,690	8	10X Genomics (v3)	Ding et al.⁶⁰	4	209
	PbmcBench (CEL-Seq)	19,754	7	CEL-Seq2	Ding et al.⁶⁰	3	559
	PbmcBench (Drop-Seq)	23,154	9	Drop-Seq	Ding et al.⁶⁰	4	102
	PbmcBench (inDrop)	21,832	7	inDrop	Ding et al.⁶⁰	3	134
Inter-dataset Benchmark	PbmcBench (Seq-Well)	18,966	7	Seq-Well	Ding et al.⁶⁰	3	102
	PbmcBench (SMARTseq)	18,886	6	SMART-Seq2	Ding et al.⁶⁰	2	569
	Xin	1449	4	SMARTer	Xin et al.⁶¹	1	46
	Baron Human	8569	14	inDrop	Baron et al.⁵³	9	7
	Segerstolpe	2133	13	SMART-s	Segerstolpe et al.⁶²	7	5
	Muraro	2122	9	CEL-Seq	Muraro et al.⁵⁴	4	3
Case study	Cardiac Atlas	487,106	11	10X Genomics	Litviňuková et al.⁴¹	5	3799
	PKU_Covid Atlas	1,462,702	64	10X Genomics	Ren et al.¹⁷	54	17

The Dataset column presents the dataset name we used in the article. The cell number column shows the total number of cells in the dataset before preprocessing. The protocol column shows the sequencing method that generates this dataset. The minor cell-type column shows the number of the cell types which has cells less than 5% of the total cell numbers. The cell number of the smallest cell-type column presents the number of cells in the cell population that has the smallest cell number. All the usages of the corresponding dataset are shown in the Application column.

Search