HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses

Nucleic Acids Research, 2023 · DOI: https://doi.org/10.1093/nar/gkac1001 · Published: November 1, 2022

Bioinformatics Research Methodology & Design

Simple Explanation

The study introduces Human Universal Single Cell Hub (HUSCH), a database integrating single-cell transcriptomic profiles from nearly 3 million cells across 45 human tissues. HUSCH uniformly processes and annotates data, providing interactive gene expression visualization, differentially expressed genes, functional analyses, and cell-cell interaction analyses. The database allows comprehensive analysis of gene expression within each tissue by integrating datasets from multiple sources and platforms, enabling users to search, visualize, analyze, and download single-cell gene expression data.

Study Duration

Not specified

Participants

Data from 185 high-quality human scRNA-seq datasets from 45 different tissues

Evidence Level

Not specified

Key Findings

1
HUSCH integrates single-cell transcriptomic profiles of nearly 3 million cells from 185 high-quality human scRNA-seq datasets across 45 different tissues.
2
HUSCH provides interactive gene expression visualization, differentially expressed genes, functional analyses, transcription regulators and cell–cell interaction analyses for each cell type cluster.
3
HUSCH allows comprehensive visualization and analysis of gene expression within each tissue based on single-cell datasets from multiple sources and platforms.

Research Summary

The Human Universal Single Cell Hub (HUSCH) is introduced as a curated database integrating single-cell transcriptomic profiles from nearly 3 million cells across 45 human tissues. HUSCH uniformly processes and annotates data with a standard workflow, offering interactive gene expression visualization and various analyses for each cell type cluster. HUSCH enables comprehensive visualization and analysis of gene expression within each tissue by integrating datasets from multiple sources and platforms, with functionalities for searching, visualizing, analyzing, and downloading single-cell gene expression data.

Practical Implications

Enhanced Understanding of Cell Types

HUSCH facilitates investigating mechanisms of cell type differentiation, disease occurrence, and progression by providing comprehensive gene expression patterns across different human cell types.

Data Reuse and Integration

The database addresses challenges in data integration and reuse by offering uniformly processed and annotated datasets, promoting efficient utilization of existing scRNA-seq data.

Advanced Functional Analysis

HUSCH provides advanced analysis functions such as functional analyses, cell–cell interactions, and transcriptional regulator analyses, enabling a deeper understanding of cell type functions and their association with phenotypes.

Study Limitations

1
Datasets containing <1000 cells were not included in the HUSCH database
2
HUSCH is aimed at normal scRNA-seq datasets from human tissues
3
HUSCH requires the users to input the gene symbol types, PC number, and clustering resolutions for pre-processing the scRNA-seq dataset online.

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