Table 1 Description of the 34 single-cell data sets used to assess the performance of computational methods.

From: Fast and precise single-cell data analysis using a hierarchical autoencoder

Data set	Tissue	Size	Class	Protocol	Accession ID	Reference
1. Yan	Human embryo	90	6	Tang	GSE36552	Yan et al., 2013⁵⁰
2. Goolam	Mouse embryo	124	5	Smart-Seq2	E-MTAB-3321	Goolam et al., 2016⁵¹
3. Deng	Mouse embryo	268	6	Smart-Seq2	GSE45719	Deng et al., 2014⁵²
4. Pollen	Human tissues	301	11	SMARTer	SRP041736	Pollen et al., 2014⁵³
5. Patel	Human tissues	430	5	Smart-Seq	GSE57872	Patel et al., 2014⁴
6. Wang	Human pancreas	457	7	SMARTer	GSE83139	Wang et al., 2016⁵⁴
7. Darmanis	Human brain	466	9	SMARTer	GSE67835	Darmanis et al., 2015⁵⁵
8. Camp (Brain)	Human brain	553	5	SMARTer	GSE75140	Camp et al., 2015⁵⁶
9. Usoskin	Mouse brain	622	4	STRT-Seq	GSE59739	Usoskin et al., 2015⁵⁷
10. Kolodziejczyk	Mouse embryo stem cells	704	3	SMARTer	E-MTAB-2600	Kolodziejczyk et al., 2015³⁷
11. Camp (Liver)	Human liver	777	7	SMARTer	GSE81252	Camp et al., 2017⁵⁸
12. Xin	Human pancreas	1,600	8	SMARTer	GSE81608	Xin et al., 2016⁵⁹
13. Baron (Mouse)	Mouse pancreas	1,886	13	inDrop	GSE84133	Baron et al., 2016⁶⁰
14. Muraro	Human pancreas	2,126	10	CEL-Seq2	GSE85241	Muraro et al., 2016⁶¹
15. Segerstolpe	Human pancreas	2,209	14	Smart-Seq2	E-MTAB-5061	Segerstolpe et al., 2016³⁸
16. Klein	Mouse embryo stem cells	2,717	4	inDrop	GSE65525	Klein et al., 2015⁶²
17. Romanov	Mouse brain	2,881	7	SMARTer	GSE74672	Romanov et al., 2017⁶³
18. Zeisel	Mouse brain	3,005	9	STRT-Seq	GSE60361	Zeisel et al., 2015³
19. Lake	Human brain	3,042	16	Fluidigm C1	phs000833.v3.p1	Lake et al., 2016⁶⁴
20. Puram	Human tissues	5,902	10	Smart-Seq2	GSE103322	Puram et al., 2017⁶⁵
21. Montoro	Human pancreas	7,193	7	Smart-Seq2	GSE103354	Montoro et al., 2018⁶⁶
22. Baron (Human)	Human pancreas	8,569	14	inDrop	GSE84133	Baron et al., 2016⁶⁰
23. Chen	Mouse brain	12,089	46	Drop-seq	GSE87544	Chen et al., 2017⁶⁷
24. Sanderson	Mouse tissues	12,648	11	10X Genomics	SCP916	Sanderson et al., 2020⁶⁸
25. Slyper	Human blood	13,316	8	10X Genomics	SCP345
26. Campbell	Mouse brain	21,086	21	Drop-seq	GSE93374	Campbell et al., 2017⁶⁹
27. Zilionis	Human lung	34,558	9	inDrop	GSE127465	Zilionis et al., 2019⁷⁰
28. Macosko	Mouse retina	44,808	12	Drop-seq	GSE63473	Macosko et al., 2015⁷¹
29. Hrvatin	Mouse visual cortex	48,266	8	inDrop	GSE102827	Hrvatin et al., 2018⁷²
30. Tabula Muris	Mouse tissues	54,439	40	10X Genomics	GSE109774	Schaum et al., 2018⁷³
31. Karagiannis	Human blood	72,914	12	10X Genomics	GSE128879	Karagiannis et al., 2020⁷⁴
32. Orozco	Human eye	100,055	11	10X Genomics	GSE135133	Orozco et al., 2020⁷⁵
33. Darrah	Human blood	162,490	14	Drop-seq	GSE139598	Darrah et al., 2020⁷⁶
34. Kozareva	Mouse cerebellum	611,034	18	10X Genomics	SCP795	Kozareva et al., 2020⁷⁷

The first two columns describe the name and tissue while the next five columns show the number of cells, number of cell types, protocol, accession ID, and reference.

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Table 1 Description of the 34 single-cell data sets used to assess the performance of computational methods.

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