Single-cell multimodal omics (scMMO) technologies, which capture multiple modalities of the same cell, have become powerful tools for unraveling cell heterogeneity. In recent years, there has been a rapid accumulation of scMMO data. However, the scMMO data is highly fragmented, which severely hindered data access and utilization.

A research team led by Prof. JIN Wenfei from the Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), constructed and released scMMO-atlas, a single-cell multimodal omics atlas to facilitate the access of scMMO data.

The research was published in Nucleic Acids Research on September 24, 2024, entitled “scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics”.

This study collected and integrated more than 70 high-quality single-cell multimodal datasets to build the scMMO-atlas (https://www.biosino.org/scMMO-atlas/). The scMMO-atlas includes scMMO data of 3,168,824 cells from 852 samples in 27 tissues/organs. scMMO-atlas provides an interactive portal for visualizing and analyzing the multiple modalities of scMMO data, such as cell annotation, cell subset specific marker genes, cell subset specific chromatin accessibility, gene module and dataset module. It also provides options for users to upload their data and download analysis results.

Construction and functional overview of scMMO-atlas. (Image by Prof. JIN Wenfei’s team)

The researchers conducted an integrated analysis of scATAC+RNA data from the mouse cerebral cortex within scMMO-atlas. An early astrocyte subset highly expressed Grm3 was identified and named as Astro-Grm3. Additionally, a progenitor of Ex-L6-Tle4 was discovered and named as Ex-L6-Tle4-Nrf1.

These findings showed the large-scale data in scMMO-atlas with enhanced statistical power and facilitated biological insights.

Comprehensive exploration of cell heterogeneity of mouse cerebral cortex by scMMO data. (Image by Prof. JIN Wenfei’s team)

“It is exciting to construct the scMMO-atlas. We hope it will significantly facilitate scMMO data usage and enhance biological discovery.”, said by CHENG Wenwen, the first author of this study.

Dr. JIN Wenfei from SINH, CAS designed this study. CHENG Wenwen, a joint Ph.D. student at Southern University of Science and Technology and SINH, is the first author of this paper. Dr. CHEN Xi and Dr. HONG Ni from Southern University of Science and Technology, provided valuable suggestions for this study. Dr. YU Shiya and Mr. YIN Changhui also contributed to the study.

This research was supported by the National Key R&D Program, the National Natural Science Foundation of China and the Biomedical Big Data Center, SINH.

Media Contact:
WANG Jin
Shanghai Institute of Nutrition and Health,
Chinese Academy of Sciences
Email: wangjin01@sinh.ac.cn
Web: http://english.sinh.cas.cn/