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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Jun 5, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.

Frederic B Bastian^1,2, Alessandro Brandulas Cammarata^1,2, Sara Carsanaro^1,2

¹Evolutionary Bioinformatics, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland.

Nucleic Acids Research

|December 10, 2024

Summary

This summary is machine-generated.

Bgee now offers comprehensive, species-comparable gene expression data, including single-cell resolution. This enhanced database aids research across diverse animal species with improved accessibility and expanded content.

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Area of Science:

Bioinformatics
Comparative Genomics
Developmental Biology

Background:

Bgee is a database for comparative gene expression patterns across animal species.
Consistent data annotation and processing enable cross-species comparisons.
Previous versions lacked comprehensive single-cell RNA sequencing data integration.

Purpose of the Study:

To integrate single-cell RNA sequencing data into Bgee for cell-resolution gene expression analysis.
To enhance cross-species gene expression data comparability.
To improve data accessibility and query capabilities for researchers.

Main Methods:

Curated integration of public single-cell RNA sequencing datasets.
Development of a new web interface with advanced querying features.
Expansion of species coverage and update of programmatic access tools.

Main Results:

Bgee now provides definitive, cell-resolution gene expression patterns comparable across species.
A new user-friendly interface allows detailed data retrieval by organ, cell type, and developmental stage.
Species count increased from 29 to 52, including fish, livestock, and nonhuman primates.

Conclusions:

Bgee offers a powerful, unified resource for comparative gene expression studies at single-cell resolution.
The updated platform enhances biological research by providing accessible and detailed cross-species data.
Expanded species coverage supports diverse research areas, from vertebrate genomics to agricultural science.