Medaka

Overview

Medaka (Oryzias latipes) is a key model organism for evolutionary developmental biology, epigenetics, and comparative genomics research. This portal provides comprehensive genomic resources including transcriptomic data, chromatin accessibility profiles, and epigenetic maps spanning embryonic development and tissue differentiation. Medaka serves as an important comparative system to zebrafish for understanding vertebrate evolution and development.

Research Areas Covered

• Embryonic Development: Transcriptional dynamics, chromatin accessibility changes during embryogenesis, phylotypic period
• Comparative Genomics: Cross-species regulatory conservation, vertebrate evolution, speciation processes
• Regenerative Biology: Heart regeneration mechanisms, immune response in tissue repair
• Reproductive Biology: Germ cell specification, gonadal development, sex determination
• Evolutionary Biology: Centromere evolution, genome structure variations, regulatory network conservation
• Stem Cell Biology: Tissue-specific stem cell populations, homeostatic functions
• Epigenetic Reprogramming: DNA methylation dynamics, primordial germ cell development, chromatin remodeling

Reference Genome and Annotation

Data Sources

Single cell data

GeneID handling describes how single-cell gene identifiers are connected to the current portal database:

• Original: keeps the author’s original identifier system.
• Converted: keeps the author matrix but converts gene identifiers to the current database when a stable mapping is available. Some features may be omitted from public display when no confident mapping exists, and renamed or merged annotations can introduce small differences relative to the author’s original feature set.
• Rebuilt: regenerates the matrix from raw reads against the current reference. This keeps identifiers consistent with the current database, but expression values, detected features, and cell annotations can differ from the author’s original workflow.

Bulk data