scAtlasLC (single-cell Atlas in Liver Cancer) is a publicly available data portal of single-cell transcriptomic profiles of tumor cell communities in hepatocellular carcinoma and intrahepatic cholangiocarcinoma.
scAtlasLC can be used to evaluate gene expression in malignant cells and various non-malignant cells in liver cancer. It can be further used to determine gene expression in different subtypes of stromal cells and immune cells.
Current single-cell data used for scAtlasLC includes the following: NCI-CLARITY (GSE151530). This cohort includes single cell transcriptomic profiles of 52,789 cells derived from 46 hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) biopsies of 37 patients. Multi-Regional (GSE189903). This cohort consists of 112,506 cells from four HCC patients and three iCCA patients. For each tumor, single cells from five separate regions, i.e., three tumor cores (T1, T2, and T3), one tumor border (B) and an adjacent normal tissue (N), were prepared. A total of 34 samples were included in this study. Sequential NCI-CLARITY (GSE229772). This cohort consists of 57,567 cells from nine HCC patients and two iCCA patients. Tumor biopsies were collected longitudinally, with two to five samples for each patient. Overall, 31 samples were collected across all patients.