Table 1.

Comparison of database features

Name of database	Species curated	Features of data resource	Features of database analytical and visualization functions
Temporal Expression during Development Database (TEDD)	human and model animal species, include mouse, zebrafish, and nematode	curation, integration and visualization of RNA-seq, scRNA-seq/scATAC-seq datasets from human and model animal species studies; focuses on providing temporal gene expression and chromatin accessibility profiles during embryonic, fetal, neonatal, childhood, and adult development.	1. temporal gene expressions in bulk-sample and single-cell levels, PCA analysis and UMAP visualization;
			2. temporal chromatin accessibilities in single-cell level, PCA analysis, and UMAP visualization;
			3. clustering of multiple genes (from the same GO or KEGG pathway) based on the expression levels;
			4. co-expression analysis;
			5. temporally regulated genes
			6. stably expressed genes
Gene Expression Omnibus (NCBI/GEO)	all species include plants and animals	archiving of raw data or expression matrics for all transcriptome sequencing resource.	Not available
Single Cell Expression Atlas (EMBL-EBI/SCEA)	animals, protists, plants and Fungi	curation and visualization of scRNA-seq/scATAC-seq studies in model and non-model species.	1. gene expression in single-cell levels, and PCA analysis;
			2. chromatin accessibilities in single-cell level, and PCA analysis;
			3. clustering of marker genes
Mouse Cell Atlas (MCA)	Mouse	single-cell RNA sequencing of major mouse organs from early embryonic stage to the mature adult stage.	1. gene expression in single-cell levels, and PCA analysis;
			2. clustering of marker genes;
			3. identifying cell types in users' data
Cell-omics Data Coordinate Platform (CDCP)	23 organisms	curation and visualization of scRNA-seq/scATAC-seq studies in model animal species.	1. gene expression in single-cell levels, and PCA analysis;
			2. clustering of marker genes;
			3. online single-cell data analysis
Single Cell Portal	10 organisms	curation and visualization of scRNA-seq/scATAC-seq studies in model and non-model species.	1. collection of single-cell genomics data;
			2. gene expression in single-cell levels, and PCA analysis
Human Gene Expression During Development (Descartes)	Human, mouse, worm and fly	scRNA-seq/scATAC-seq for human and model species development; for human, focuses on 15 organs in fetal samples	1. collection of scRNA and scATAC data;
			2. gene expression in single-cell levels, and PCA analysis;
			3. exploration on cell trajectory for organ development
Human Cell Atlas Portal (HCA)	Human	scRNA-seq/scATAC-seq/snRNA-seq for mapping the human body at the cellular level; focuses on data collection of single-cells derived from 9 human tissue-types and immune system	1. collection of scRNA and scATAC data from human tissues or diseases;
			2. gene expression in single-cell levels, and PCA analysis;
Cancer Single-cell Expression Map (CancerSCEM)	Human	focuses on cancer samples	1. gene expression in single-cell levels, and PCA analysis;
			2. gene correlation;
			3. cell component comparison;
			4. cell interaction network;
			5. survival analysis
Single-Cell Transcriptome for human diseases (SC2disease)	Human	focuses on human multiple diseases and cancer studies	1. providing browse for the expression of interested genes;
			2. searching for cell-type markers;
			3. searching for the biomarkers of multiple diseases;
			4. comparing the expression profiles of various types of cells in disease and non-disease states
Deeply Integrated human Single-Cell Omics data (DISCO)	Human	focuses on 14 tissue types in human and PBMC samples in COVID-19 atlas	1. data exploration at sample and integrated level;
			2. CELLiD cell type identification;
			3. online integration;
			4. mapping user single-cell data to a specific atlas with Cell Mapper.
Single-cell atlases for exposing molecular characteristics of COVID-19 (SCovid)	COVID-19	focuses on COVID-19 across 10 human tissues	1. providing a browser of the molecular characteristics of COVID-19 on independent datasets of different tissues;
			2. obtaining the molecular roles in different tissues by searching genes;
			3. obtaining significantly differentially expressed genes in a specific cell type;
			4. providing access of differentially expressed genes' expression profiles based on single-cell datasets of COVID-19 and controls
The Genotype-Tissue Expression (GTEx)	Human	genome sequencing and exome sequencing, RNA-Seq and snRNA-seq; focuses on differential expressions among different tissue-types for human adult cases	1. gene expression in bulk-sample and single-cell levels, and PCA analysis;
			2. providing enquiry and visualization of the QTLs by gene/variant in the Locus Browser
			3. providing a browser of H3K27ac ChIP-seq, m6A methylation, and WGBS DNA methylation data in IGV Browser
			4. providing search and request for the GTEx archived biospecimens