CellMarker: a manually curated resource of cell markers in human and mouse

Abstract

One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100 000 published papers, 4124 entries including the cell marker information, tissue type, cell type, cancer information and source, were recorded. At last, 13 605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues were collected and deposited in CellMarker. CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph. We believe that CellMarker is a comprehensive and valuable resource for cell researches in precisely identifying and characterizing cells, especially at the single-cell level.

Highly ACE2 Expression in Pancreas May Cause Pancreas Damage After SARS-CoV-2 Infection

“…All of scRNA-seq data analysis was based on Seurat R package (version: 3.1.4) with the default parameters [10]. The annotation of cell types was completed based on the featured genes of each cluster and the cell markers of each type pancreas cell from CellMarker database [11] and previously report [8,9].…”

Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2

“…Expression of the ACE2 gene was mapped onto cluster figures to determine overlap with previously identified cell types or cell type marker genes identified in the literature. Cell type was mapped by expression of known marker genes of cell types expressed in the lung and small intestine, as defined by lists derived from the literature as curated in the CellMarker database (42).…”

Strategy for achieving standardized bone models

“…Since not all cells react in the same way to chemical and mechanical stimuli, it is essential to validate the parameters of the system with the cell type(s) (Bouet, Marchat, et al, ) most adapted to the scientific question or intended application. As a key component of the 3D culture system, the cells used have to be thoroughly sorted and selected, for instance with antibodies targeting cell‐specific surface markers (Camilleri et al, ; Zhang et al, ).…”