Table 2.
Summary of human liver scRNA-seq studies and the NK cell clusters identified.
| References | Year | Journal | Sample type | Technology platform | Cells sequenced | GEO dataset ID | NK cell clusters | Descriptor of gene sets available |
|---|---|---|---|---|---|---|---|---|
| Zhao et al. (36) | 2020 | Cell Discovery | Liver perfusate obtained during orthotopic liver transplantation (n = 3); Fresh | Library = 10X Genomics, Sequenced = Illumina Hiseq XTEN platform | Magnetically sorted CD45+ cells | GSE125188 | Clusters 12 and 13; Figure 2, Supplementary Table 4 | DEG comparing CXCR6+ NK vs. CX3CR1+ NK cell clusters (up-regulated genes in each cluster) |
| Zhang et al. (40) | 2020 | Journal of Hepatology | Treatment naïve-ICC tissues and paired adjacent normal samples | Library = 10X Genomics, Sequenced = Illumina Xten or NovaSeq 6000 system | Viable single cell suspension post tissue digestion | GSE138709, GSE142784 | NK cell; Supplementary Table 2 | DEG comparing NK cell cluster vs. all other clusters (no information on up- or down-regulation) |
| Aizarani et al. (38) | 2019 | Nature | Healthy liver tissue obtained during resections for CRC metastasis or CC (n = 9); Cryopreserved and fresh | mCEL-Seq2 | PHH and NPCs or sorted directly after tissue digestion if HCC sample. | GSE124395 | Cluster 5; Supplementary Table 1 | DEG comparing NK cell cluster vs. all other clusters (up- and down-regulated genes) |
| Ramachandran et al. (39) | 2019 | Nature | Healthy liver tissue obtained during resections for CRC metastasis (n = 5) Cirrhotic tissue obtained during orthotopic liver transplantation (n = 5); Fresh | Library = 10X Genomics/Sequenced= Illumina HiSeq 4000 | Viable CD45+ leucocytes vs. CD45− non-parenchymal cells were sorted via FACS | GSE136103 | Clusters NK cell (1), NK cell (2), and cNK cell; Extended Data Figure 3E, Supplementary Table 6 | DEG comparing each NK cell cluster vs. all other clusters (up-regulated genes in each cluster) |
| MacParland et al. (37) | 2018 | Nature Communictions | Healthy liver tissue obtained during orthotopic liver transplantation (n = 5); Fresh | Library = 10X Genomics/Sequenced= Illumina HiSeq 2500 | Total liver homogenate | GSE115469 | Cluster 8; Supplementary Data 1 | DEG comparing NK cell cluster vs. all other clusters (up- and down-regulated genes) |
CRC, Colorectal cancer; CC, cholangiocarcinoma; PHH, primary human hepatocytes; NPCs, non-parenchymal cells; FACS, fluorescence-activated cell sorting; DEG, differentially-expressed genes.