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Using NovelBrain single cell cloud to explore the distribution of receptor ACE2 of new crown virus in human organs Time: 2020-03-16

At present, the infection of the new coronavirus is still in a stalemate. In order to develop new drugs for the treatment of new crown virus as soon as possible, scientists have been constantly involved in clinical research and 菜鸟竞技平台 to understand and understand the pathogenesis of the new crown virus. The new coronavirus is similar to the SARS virus, and it plays a role through the incorporation of ACE2 receptor into human cells. The presence of ACE2 in the lung may become the main target of the virus, but a number of patients also have symptoms of organ dysfunction. A few days ago, the lancet Lancet Respiratory Medicine The clinical progress and related research findings of 52 new crown pneumonia critical patients included in the Wuhan Jin Yin Tan Hospital were published. It was found that 15 (29%) of them had acute kidney injury, 12 (23%) had cardiac injuries, and 15 (29%) had abnormal liver function. Therefore, understanding the distribution and expression level of ACE2 in human tissues is of certain significance to the mechanism of parsing virus.

The single cell sequencing technology, which describes the cellular maps of human organs and single cell public data, plays a key role in characterizing the distribution of ACE2 in human organs and tissues.

In this issue, we downloaded several sets of public single cell sequencing data from functional organs. Novelbrain Look at the single cell cloud platform. ACE2 And describes the further direction of mining using the analysis of health information.


One Study on liver tissue cell Atlas

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).


Fig. 1 cell type identification of liver tissue

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).

Fig. 2 expression and distribution of ACE2

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).

Fig. 3 re-cluster of bile duct cell subsets

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.)

Fig. 4 further analysis of ACE2


2. cell mapping of lung tissue



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.



Analysis result



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).



Figure 5. ACE2 is mainly expressed in II type alveolar epithelial cells.


3. cell mapping of renal tissue

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.

Analysis result

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.

According to the existing data, we can see that in addition to the lung tissue, there are also ACE2 cells in the remaining two organs, which are mainly bile duct cells and proximal renal tubules, suggesting that these two types of cells will also become potential targets of infection, and may cause clinical symptoms of organ dysfunction.


All the results obtained from the above analysis are publicly displayed through single cell browsers and included in the NovelBrain CellAtlas.

This database platform can not only view the expression and distribution of ACE2, but also retrieve any genes you are interested in.

Website: Http://cellatlas.novelbrain.com/


Single cell cloud platform analysis tutorial
(1) five kernels? Yolk? BD Rhapsody? 10 x Genomics? How to select the sorting platform?
2. @ strong ice organisms, please give me a single cell transcriptome sequencing data analysis strategy.
(3) scRNA-Seq data analysis.
(4) analysis of ScRNA-Seq|| single cell transcriptome data by quasi sequential analysis
SCENIC analysis of single cell transcriptome data analysis -- searching for the driving genes in cell population

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