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Table 2 Overview of the datasets used during this study

From: A comparison of automatic cell identification methods for single-cell RNA sequencing data

Dataset No. of cells No. of genes No. of cell populations (> 10 cells) Description Protocol Reference
Baron (Mouse)a 1886 14,861 13 (9) Mouse pancreas inDrop [30]
Baron (Human)a,b 8569 17,499 14 (13) Human pancreas inDrop [30]
Muraroa,b 2122 18,915 9 (8) Human pancreas CEL-Seq2 [31]
Segerstolpea,b 2133 22,757 13 (9) Human pancreas SMART-Seq2 [32]
Xina,b 1449 33,889 4 (4) Human pancreas SMARTer [33]
CellBench 10Xa,b 3803 11,778 5 (5) Mixture of five human lung cancer cell lines 10X chromium [34]
CellBench CEL-Seq2a,b 570 12,627 5 (5) Mixture of five human lung cancer cell lines CEL-Seq2 [34]
TMa 54,865 19,791 55 (55) Whole Mus musculus SMART-Seq2 [6]
AMBa 12,832 42,625 4/22/110 (3/16/92) Primary mouse visual cortex SMART-Seq v4 [35]
Zheng sorteda 20,000 21,952 10 (10) FACS-sorted PBMC 10X CHROMIUM [36]
Zheng 68Ka 65,943 20,387 11 (11) PBMC 10X CHROMIUM [36]
VISpb (Mouse) 12,832 42,625 3/36 (3/34) Primary visual cortex SMART-Seq v4 [35]
ALMb (Mouse) 8758 42,461 3/37 (3/34) Anterior lateral motor area SMART-Seq v4 [35]
MTGb (Human) 14,636 16,161 3/35 (3/34) Middle temporal gyrus SMART-Seq v4 [37]
PbmcBench pbmc1.10Xv2b 6444 33,694 9 (9) PBMC 10X version 2 [38]
PbmcBench pbmc1.10Xv3b 3222 33,694 8 (8) PBMC 10X version 3 [38]
PbmcBench pbmc1.CLb 253 33,694 7 (7) PBMC CEL-Seq2 [38]
PbmcBench pbmc1.DRb 3222 33,694 9 (9) PBMC Drop-Seq [38]
PbmcBench pbmc1.iDb 3222 33,694 7 (7) PBMC inDrop [38]
PbmcBench pbmc1.SM2b 253 33,694 6 (6) PBMC SMART-Seq2 [38]
PbmcBench pbmc1.SWb 3176 33,694 7 (7) PBMC Seq-Well [38]
PbmcBench pbmc2.10Xv2,b 3362 33,694 9 (9) PBMC 10X version 2 [38]
PbmcBench pbmc2.CLb 273 33,694 5 (5) PBMC CEL-Seq2 [38]
PbmcBench pbmc2.DRb 3362 33,694 6 (6) PBMC Drop-Seq [38]
PbmcBench pbmc2.iDb 3362 33,694 9 (9) PBMC inDrop [38]
PbmcBench pbmc2.SM2b 273 33,694 6 (6) PBMC SMART-Seq2 [38]
PbmcBench pbmc2.SWb 551 33,694 4 (4) PBMC Seq-Well [38]
  1. aUsed for intra-dataset evaluation
  2. bUsed for inter-dataset evaluation