CODEX

CODEX aggregates and uniformly processes public next-generation sequencing (NGS) datasets to enable comparative analysis of transcriptional programs and chromatin regulation.

Key Features:

• Centralized compendium: Aggregates multi-centre public NGS datasets into a single curated repository.
• Uniform processing: Applies consistent processing to enable direct comparability of datasets across laboratories.
• Rigorous vetting: Implements curation and quality-control procedures to identify and retain high-quality samples.
• Experiment coverage: Includes transcription factor ChIP-Seq, histone modification ChIP-Seq, DNase-Seq, and RNA-Seq datasets.
• Specialized repositories: Organizes datasets into HAEMCODE and ESCODE focusing on haematopoiesis and embryonic stem cell samples, respectively.
• Scale and scope: Hosts over 1,000 samples encompassing data from 221 transcription factors and 93 distinct cell types.
• Reference compendium: Serves as a comparative reference for analyses of TF binding, histone modifications, chromatin accessibility, and transcriptomes.

Scientific Applications:

• Transcriptional program analysis: Comparative study of transcriptional programs that govern cellular identity and fate during mammalian development.
• Chromatin regulation studies: Investigation of chromatin states and histone modification patterns across cell types and conditions.
• Haematopoiesis research: Use of HAEMCODE datasets to study regulatory networks and TF binding in blood cell development.
• Embryonic stem cell biology: Use of ESCODE datasets to investigate transcriptional and chromatin regulation in embryonic stem cells.
• Disease and homeostasis: Comparative analyses linking transcriptional and chromatin changes to homeostasis and disease contexts.

Methodology:

Public NGS datasets (transcription factor ChIP-Seq, histone modification ChIP-Seq, DNase-Seq, RNA-Seq) are collected, uniformly processed, and rigorously vetted.