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Table 1 Benchmark datasets

From: Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis

Dataset Technology Organism N cells Cell types N types Ref.
Zhengmix4eq 10x Human 3,909 B (24.5%), Monocytes (24.5%), cytoT (25.5%), rT (25.5%) 4 [11, 21]
Zhengmix4uneq 10x Human 6,345 B (15%), Monocytes (30%), cytoT (8%), rT (46%) 4 [11, 21]
Zhengmix5eq 10x Human 4,876 hT (20%), mT (20%), cytoT (20%), nT (20%), rT (20%) 5 [21]
Zhengmix8eq 10x Human 3,908 B (12.5%), Monocytes (14.5%), hT (10%), NK (15%), mT (12.5%), cytoT (10%), nT (13%), rT (12.5%) 8 [11, 21]
Zhengmix8uneq 10x Human 6,350 B (7.5%), Monocytes (15%), hT (8%), NK (4%), mT (15%), cytoT (4%), nT (23%), rT 8 [21]
sc_10x 10x Human 902 H1975 (34.5%), H2228 (35%), HCC827 (30.5%) 3 [12]
sc_10x_5cl 10x Human 3,918 A549 (32%), H1975 (11%), H2228 (19.5%), H838 (22.5%), HCC827 (15%) 5 [12]
sc_celseq2 CEL-Seq2 Human 274 H1975 (41%), H2228 (29.5%), HCC827 (29.5%) 3 [12]
sc_celseq2_5cl CEL-Seq2 Human 895 A549 (36%), H1975 (14.5%), H2228 (14%), H838 (22%), HCC827 (13.5%) 5 [12]
TabulaMuris Smart-Seq2 Murine 12,081 Brain (36.5%), intestine (31.5%), skin (19%), spleen (13%) 4 [22]
  1. The first five datasets are derived from [21] and [11] and contain CD19+ B cells (B), CD14+ monocytes (Monocytes), CD4+ helper T cells (hT), CD56+ natural killer cells (NK), CD4+/CD45RO+ memory T cells (mT), CD8+/CD45RA+ naive cytotoxic T cells (cytoT), CD4+/CD45RA+/CD25 − naive T cells (nT), and CD4+/CD25+ regulatory T cells (rT). The four next are from [12] and contain the five following cell lines: A549, H1975, H2228, H838, and HCC827. The last one is from [22]