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. 2023 Sep 1;12(1):79–90. doi: 10.14218/JCTH.2023.00224

Fig. 1. Flow diagram of different single-cell approaches in clinical liver samples.

Fig. 1

Single-cell suspension preparation: single-cell comes from fresh samples including liquid (peripheral blood, ascites) and tissue (liver cancer, adjacent tumor, normal liver) by dissociation; frozen samples can be used to snRNA-seq and ST. ST: frozen liver tissue samples are sectioned, fixed, and permeated, then transcripts are barcoded according to their location based on a matrix of spots. These barcodes are then used to show the spatial gene signatures across the tissue section. SCoPE-MS: surviving single-cell is lysed by ultrasound, proteins are extracted from the lysate then trypsinized, and peptides from multiple samples are identified and quantified using TMTs. CITE-seq: a technology consisting of mRNA and tagged antibody sequencing, which enables the simultaneous determination of unbiased transcriptional profiles and protein markers based on oligo-tagged antibody detection in a cell. ScATAC-seq: a technique for studying open chromatin regions with epigenetic and gene regulatory roles at the single-cell level. Tn5 transposase is used to cleave accessible DNA regions of open chromatin in the nuclear suspension of sorted cells, followed by post-PCR sequencing using tags of known sequence. Cell sorting: the platforms used for cell sorting are mainly based on microfluidic or cellular plate technologies, both of which allow for unbiased quantification of gene expression with the aid of unique molecular identifier and cell label technology, where mRNA expression profiles of TCR and BCR can be determined in T and B cells for adaptive immune response analysis. 10×,10× Genomics; BCR, B-cell receptor; CITE-seq, cellular indexing of transcriptome and epitopes by sequencing; PCR, polymerase chain reaction; scATAC-seq, single-cell assay for transposase-accessible chromatin with high throughput sequencing; SCoPE-MS, single-cell proteomics by mass spectrometry; scRNA-seq, single-cell RNA sequencing; snRNA-seq, single nuclear sequencing; ST, spatial transcriptome technology; TMTs, tandem mass spectrometry tags; TCR, T-cell receptor.