Table 4.
Summary of scRNA-seq datasets
| Dataset | # of genes | # of cells | # of clusters | Cells in each cluster | Standard | Cell resource | Recommended methods | |
|---|---|---|---|---|---|---|---|---|
| 1 | Biase’s [77] | 25 737 | 49 | 3 | 9 + 20 + 20 | Bench | Two and four-cell Mouse embryo |
SC3, pcaReduce and SINCERA |
| 2 | Yan’s [78] | 20 214 | 124 | 7 | 3 + 3 + 6 + 12 + 20 + 16 + 30 |
Bench | Human preimplantation embryos and embryonic stem cells | pcaReduce |
| 3 | Goolam’s [79] | 41 480 | 124 | 5 | 6 + 64 + 42 + 6 + 6 | Bench | Four-cell mouse embryos | pcaReduce |
| 4 | Deng’s [80] | 22 457 | 268 | 10 | 50 + 14 + 37 + 8 + 43 + 10 + 30 + 12 + 60 + 4 |
Bench | Mouse preimplantation embryos | SC3 and pcaReduce |
| 5 | Pollen’s [67] | 23 730 | 301 | 11 | 22 + 17 + 11 + 37 + 31 + 54 + 24 + 40 + 24 + 15 + 25 |
Bench | Human | SC3, SIMLR and pcaReduce |
| 6 | Kolodziejczyk’s [81] |
38 653 | 704 | 3 | 295 + 159 + 250 | Bench | Mouse embryonic stem cell | SC3, SINCERA and SEURAT |
| 7 | Treutlein’s [82] | 23 271 | 80 | 5 | 41 + 14 + 12 + 11 + 3 | Computational | Human lung epithelium | SC3 |
| 8 | Ting’s [83] | 29 018 | 149 | 7 | 24 + 41 + 11 + 34 + 12 + 12 + 15 |
Computational | Human pancreatic circulating tumor cells | SC3 |
| 9 | Patel’s [84] | 5948 | 430 | 5 | 118 + 94 + 75 + 73 + 70 | Computational | Human glioblastomas | SC3, tSNE+kmeans and SINCERA |
| 10 | Usoskin’s [85] | 25 334 | 622 | 11 | 125 + 233 + 26 + 48 + 12 + 17 + 32 + 64 + 22 + 31 + 12 |
Computational | Human neuron | SC3 |
| 11 | Klein’s [86] | 24 175 | 2717 | 4 | 933 + 303 + 683 + 798 | Computational | Human embryonic stem cells | SC3, tSNE+kmeans and SINCERA |
| 12 | Zeisel’s [75] | 19 972 | 3005 | 9 | 290 + 390 + 948 + 820 + 98 + 175 + 198 + 26 + 60 |
Computational | Mouse cortex | SC3 |