Related Experiment Video
Updated: Jun 17, 2026
07:27
Transcriptome Analysis of Single Cells
Published on: April 25, 2011
30.0K
HTCA: a database with an in-depth characterization of the single-cell human transcriptome
Lu Pan1,2, Shaobo Shan3, Roman Tremmel4,5
1Institute of Environmental Medicine, Karolinska Institutet, Solna 17165, Sweden.
Nucleic Acids Research
|September 21, 2022
Summary
The HTCA database integrates 2.3 million cells from 3000 single-cell RNA sequencing samples, offering deep phenotype profiles for adult and fetal tissues. This resource enables comprehensive multi-omics exploration and flexible single-cell analysis.
Area of Science:
- Genomics
- Bioinformatics
- Cell Biology
Background:
- Single-cell RNA sequencing (scRNA-seq) generates vast datasets with potential for large-scale integration and population-representative studies.
- Existing data consolidation efforts often focus on raw data or gene expression queries, lacking extensive characterization.
- A comprehensive, interactive resource for exploring multi-omics single-cell data across diverse tissue types is needed.
Purpose of the Study:
- To present HTCA, an interactive database providing in-depth phenotype profiles from millions of high-quality single cells.
- To enable comprehensive, real-time exploration of multi-omics data from adult and fetal tissues.
- To offer integrated online analysis tools for single-cell RNA sequencing (scRNA-seq) workflows.
Main Methods:
- Construction of an interactive database (HTCA) using approximately 2.3 million high-quality cells from around 3000 scRNA-seq samples.
- Integration of diverse single-cell omics data, including transcriptomics, splicing variants, spatial transcriptomics, and scATAC-seq, across 19 adult and fetal tissues.
- Development of a user-friendly interface for querying gene signatures, transcription factor activities, receptor-ligand interactions, and gene ontology (GO) terms.
Main Results:
- HTCA provides in-depth phenotype profiles for 19 healthy adult and matching fetal tissues.
- The database enables interactive queries for gene signatures, TF activities, TF motifs, receptor-ligand interactions, and GO terms across cell types.
- HTCA integrates single-cell splicing variant, spatial transcriptomics, and scATAC-seq profiles for multiple tissues, alongside scRNA-seq data.
- Online analysis tools are provided for common scRNA-seq analysis steps.
Conclusions:
- HTCA serves as a valuable, interactive resource for exploring multi-omics single-cell data from adult and fetal tissues.
- The database facilitates real-time, in-depth phenotypic characterization and comparative analyses.
- HTCA empowers researchers with integrated data and tools for flexible and comprehensive single-cell analysis.
