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Updated: Jun 11, 2025

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Published on: March 1, 2017

PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization.

Zhiting Wei^1,2, Duanmiao Si^1,2, Bin Duan^1,2

¹State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 200092, China.

Nucleic Acids Research

|October 8, 2024

Summary

This summary is machine-generated.

PerturBase is a new comprehensive database for single-cell perturbation (scPerturbation) data. It enables researchers to analyze and visualize genetic and chemical perturbation effects across millions of cells.

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Automating Aggregate Quantification in Caenorhabditis elegans

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Area of Science:

Genomics
Systems Biology
Bioinformatics

Background:

Single-cell perturbation (scPerturbation) sequencing integrates single-cell tools with bulk screening for high-resolution biological analysis.
Existing methods allow dissection of perturbation effects but lack a dedicated data repository.

Purpose of the Study:

To introduce PerturBase, a comprehensive database for scPerturbation data analysis and visualization.
To address the gap in centralized resources for exploring perturbation effects in biological systems.

Main Methods:

Curated 122 datasets from 46 studies, encompassing 24,254 genetic and 230 chemical perturbations from ~5 million cells.
Developed 'Dataset' and 'Perturbation' modules for quality control, denoising, differential gene expression, and functional analysis.
Integrated user-friendly web interfaces with interactive plots and tables for data exploration.

Main Results:

PerturBase offers a centralized platform for 115 single-modal and 7 multi-modal scPerturbation datasets.
The database facilitates analysis of perturbation-induced gene expression changes and functional impacts.
Provides tools for characterizing relationships between various genetic and chemical perturbations.

Conclusions:

PerturBase is a pioneering, high-content database for searching, visualizing, and analyzing scPerturbation data.
It significantly enhances the understanding of perturbation effects in biological systems.
Facilitates deeper insights into gene regulation and cellular responses to perturbations.