Title: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage intrahepatic
Journal and publication time: Nature Communication, October 2018
Sample and data analysis: samples were obtained from 5 donors, digested and captured by single cell with 10 x Genomics platform. Finally, 8437 cells were analyzed. (8444 articles were obtained from the analysis. The Novelbrain single cell analysis platform filtered some low expression cells during the analysis.
Analysis results: Marker through single cell browser (SingleCell Browser) The expression of Gene can be retrieved, and the cell types can be identified preliminarily. There are hepatocytes, sinusoidal endothelial cells, bile duct cells, macrophages, T cells, NK cells, B cells, plasma cells and a small number of red blood cells. A t-SNE map of cell types is defined directly on the browser and Bubble Plot of Marker Gene (Fig. 1).
The expression of ACE2 gene was found to be mainly expressed in some bile duct cells, and the t-SNE map of the gene was obtained by single cell browser to describe its expression and distribution characteristics (Fig. 2).
As can be seen from the above, ACE2 is only expressed in some cells of bile duct cells, so we can make a more detailed classification of the cluster of cholangiocarcinoma by re-cluster based on the single cell analysis platform. A total of three subsets were obtained, and it was found that ACE2 specificity was expressed in only one cluster (Fig. 3).
Next, we can conduct a series of in-depth analysis of this ACE2 positive cell subgroup to explore the characteristics of the subgroup and the downstream functions that ACE2 may open after receiving the signal. By analyzing the regulatory characteristics of transcription factors (previous title and links) by SCENIC, it is found that the group is regulated by a number of transcription factors (Fig. 4A). At the level of gene expression, differential genes and possible potential effects of ACE2 positive bile duct cell population and ACE2 negative bile duct cell population can be obtained through differential gene analysis (Fig. 4B), and the difference in pathway activation degree is obtained by scoring method (Fig. 4C). Differential gene analysis revealed that. In addition, co expression analysis can also identify genes co expressed with ACE2 and possible downstream regulatory mechanisms (Fig. 4D). (strong ice organisms also support more customized in-depth analysis, through the end of the mail or telephone to get more information.)
Title: Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology the
Published journals: Am J Respir Crit Care Med
Publication time: June 2019
Sample and data analysis : The samples were obtained from 8 donors, digested and single cell capture by 10 x Genomics platform. Finally, 43558 cells were obtained.
Marker through single cell browser (SingleCell Browser) The expression of Gene could be used to identify cell types. I type alveolar epithelial cells (mixed with a small number of basal cells and rod cells, subdivided), II alveolar epithelial cells, ciliated cells, endothelial cells, fibroblasts, monocytes, macrophages, dendritic cells, T cells, B cells, plasma cells and some submersible cells were found. The double cell population (expressed simultaneously in two cell types of Marker). By searching for the expression of ACE2, it was found that it was mainly expressed in type II alveolar epithelial cells. (Fig. 5).
Title: Comparative analysis and refinement of human PSC-derived kidney organoid differentiation with differentiation
Published journals: Cell Stem Cell
Publication time: December 2018
Sample and data analysis : The samples were derived from 1 donors cells, and the nuclei were obtained by single cell capture by 10 x Genomics platform. Finally, 4524 cells were obtained.
The expression of Marker Gene was retrieved by single cell browser (SingleCell Browser), and the cell types could be preliminarily identified. There were proximal renal tubules, connective tubules, collecting ducts, distal convoluted tubules, podocytes, Henry's loops, and moistening cells. By searching for the expression of ACE2, it was found that it was mainly expressed in proximal renal tubules (Fig. 6).
Figure 6. ACE2 is mainly expressed in proximal renal tubules.
Single cell cloud platform analysis tutorial 2. @ strong ice organisms, please give me a single cell transcriptome sequencing data analysis strategy. SCENIC analysis of single cell transcriptome data analysis -- searching for the driving genes in cell population