CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Publicly available next-generation sequencing (NGS) data is rapidly increasing.
• A unified platform for accessing and comparing diverse NGS datasets is needed.
• Experimental biologists require user-friendly tools for genomic data interrogation.

Purpose of the Study:

• To establish CODEX, a centralized, user-friendly database for publicly available NGS data.
• To provide uniformly processed and directly comparable NGS datasets.
• To facilitate the interrogation of transcriptional programs regulating cellular processes.

Main Methods:

• Development of a comprehensive database (CODEX) integrating multiple NGS experiment types.
• Uniform processing and vetting of all deposited samples.
• Implementation of visualization and data comparison tools.

Main Results:

• CODEX provides access to over 1000 uniformly processed NGS samples.
• The database includes transcription factor ChIP-Seq, histone modification ChIP-Seq, DNase-Seq, and RNA-Seq data.
• CODEX contains data on 221 unique transcription factors and 93 unique cell types, with specialized repositories HAEMCODE and ESCODE.

Conclusions:

• CODEX serves as a valuable resource for the scientific community, offering high-quality, comparable NGS data.
• The database facilitates the study of transcriptional regulation in mammalian development, homeostasis, and disease.
• CODEX empowers researchers to visualize, download, and compare datasets for deeper biological insights.