Environmental DNA (eDNA) Metabarcoding Dataset from Urban and Protected Coastal Waters in Jakarta Bay, Indonesia

These include two urban-impacted locations (Tanjung Priok Port and Untung Jawa Island) and two sites within the Seribu Islands National Marine Park (Pramuka and Harapan Islands). Water samples were collected in triplicate at each site, and eDNA was extracted using the Qiagen DNeasy Blood and Tissue Kit protocol.

PCR amplification targeted the mitochondrial cytochrome c oxidase subunit I (COI) gene using universal primers. Sequencing was performed on the Illumina MiSeq platform, and sequence processing followed the MBRAVE pipeline with taxonomic assignment referencing BOLD and NCBI databases. This dataset supports the manuscript entitled "Urbanization Reshapes Marine Biodiversity: eDNA Insights from Jakarta Bay", submitted to Scientific Reports.