MMETSP: Marine Microbial Eukaryote Transcriptome Assemblies

The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) dataset contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla. It provides de novo transcriptome assemblies, peptide translations, gene annotations, and gene expression quantifications for these organisms. The data was generated using methods described in the Eel Pond khmer protocols and associated scripts are available on GitHub.

Use Cases

• Comparative transcriptomics across more than 40 eukaryotic phyla based on the described taxonomic breadth.
• Functional annotation of marine microbial genes using the provided GFF annotation files.
• Gene expression analysis in marine eukaryotes using the Salmon quantification files.
• Testing and benchmarking de novo transcriptome assembly pipelines based on the referenced Eel Pond protocols.

Strengths

• Represents a broad taxonomic diversity, covering cultured samples from more than 40 eukaryotic phyla.
• Provides multiple linked data types including assemblies, annotations, and quantifications for integrated analysis.
• Methods are documented in published protocols (Brown et al. 2015) and scripts are publicly available on GitHub.

Limitations

• Key metadata such as row count, file size, specific column names, and last update date are unknown across all sources.
• The dataset's license is described only as 'Open Access (green)', which lacks precise terms (e.g., CC-BY).
• Descriptions are repetitive across platforms, suggesting sparse or auto-populated metadata.

Provenance

Source

Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP), University of California, Davis.

Collection Method

Cultured samples were sequenced and assembled de novo using the Trinity assembler and methods from the Eel Pond khmer protocols.

Geography

Marine environments (pelagic and endosymbiotic habitats).