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Updated: Jul 9, 2025

Massively Parallel Reporter Assays in Cultured Mammalian Cells
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MPRAbase: A Massively Parallel Reporter Assay Database.

Jingjing Zhao1,2, Fotis A Baltoumas3, Maxwell A Konnaris4,5

  • 1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.

Biorxiv : the Preprint Server for Biology
|December 4, 2023
PubMed
Summary
This summary is machine-generated.

Massively parallel reporter assays (MPRAs) measure gene regulatory activity. MPRAbase is a new database consolidating MPRA experiment data for easier access and analysis.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Massively parallel reporter assays (MPRAs) are high-throughput technologies for assessing gene regulatory elements.
  • MPRAs have diverse applications, including regulatory element discovery and variant effect analysis.
  • A lack of a centralized database hinders the accessibility and integration of MPRA data.

Purpose of the Study:

  • To develop MPRAbase, a manually curated database for MPRA experimental results.
  • To provide a centralized, user-friendly platform for accessing and analyzing MPRA data.
  • To facilitate the sharing and dissemination of published MPRA data within the research community.

Main Methods:

  • Manual curation of published MPRA experiments.
  • Data compilation including sequences, regulatory activity, cell types, and organisms.
  • Development of a web interface for data access and download.

Main Results:

  • MPRAbase currently contains 129 experiments with 17,718,677 tested elements.
  • Data spans 35 cell types and 4 organisms.
  • The web interface allows users to download data for independent analysis.

Conclusions:

  • MPRAbase serves as a valuable resource for researchers studying gene regulation.
  • The database promotes data sharing and accelerates scientific discovery in the MPRA field.
  • MPRAbase enhances the utility of MPRA data by centralizing and organizing experimental results.