DOI: 10.5281/zenodo.15178203
title: Cyclonephilic ProA

description: This data repository contains supplementary data supporting the manuscript titled "Mesoscale eddies shape Prochlorococcus population dynamics in the open ocean". Each data file was generated or analyzed to explore Prochlorococcus community structure and function, ecotype distribution, and functional gene expression in cyclonic vs. anticyclonic eddies in the North Pacific Subtropical Gyre.

 
description: File list:

170801_MESOSCOPE_DigitizedLogbookFinal20190508.txt

Metadata for metatranscriptomic samples collected during the 2017 MESO-SCOPE cruise. Each row corresponds to a unique seawater sample collected at specific depths, locations, and times of day, along with associated processing metadata. Sample identifiers (e.g., MSR00-20a-DL-SL2C30-0015) match metatranscriptomic data files. In these identifiers, -SL1 denotes cyclone samples and -SL2 denotes anticyclone samples; C# indicates the cast number; and the suffix -015 or -DCM refers to samples collected at the surface (15 m) or deep chlorophyll maximum (DCM), respectively. This dataset enables precise alignment of transcriptomic profiles with environmental, temporal, and methodological metadata, supporting robust ecological and statistical analyses.

MetaT_normalization.factors.txt

Sample-specific normalization factors derived solely from ERCC (External RNA Control Consortium) spike-in standards. Each row lists a unique metatranscriptomic sample and its corresponding normalization factor, which accounts for technical variability in RNA extraction efficiency, library preparation, and sequencing depth. These values are used to normalize transcript counts across samples, enabling accurate comparisons of gene expression levels independent of methodological bias.

 

metaG.ms.pcc.cluster_reps.clades.tsv

Clade-level taxonomic annotations for representative Prochlorococcus gene clusters identified in metagenomic datasets from the MESO-SCOPE cruise. Each row corresponds to a unique gene cluster (e.g., MSD00-20a-VH-SL1C33-0084_c50_1), with associated taxonomic information including: Taxonomic identifier (taxid) based on GTDB v95, Organism name and genus assignment (e.g., Prochlorococcus_A), Assigned clade (e.g., HL for high-light-adapted clades).

metaG.ms.pcc.fna.100.emap.w_best.tsv

Functional and taxonomic annotations for gene contigs derived from Prochlorococcus-enriched metagenomic assemblies collected during the MESO-SCOPE cruise. Each row represents a predicted gene, and columns include: Query identifiers linked to contigs (query), Top matching orthologs (seed_ortholog, eggNOG_OGs, COG, KEGG_ko), Alignment metrics (evalue, score), Functional annotations across multiple databases: eggNOG, COG, KEGG, PFAM, EC numbers, Gene Ontology (GOs), Metabolic pathways (KEGG_Pathway, KEGG_Reaction, KEGG_Module), Transporters (KEGG_TC), carbohydrate-active enzymes (CAZy), and BiGG metabolic reactions, Clade-level lineage assignments from hierarchical orthology groups

 

MetaT_Prochlorococcus_A_ERCC_Vol_Norm.xlsx

Normalized metatranscriptomic read counts for Prochlorococcus A genes collected from the deep chlorophyll maximum (DCM) of adjacent cyclonic and anticyclonic eddies in the North Pacific Subtropical Gyre. Transcript abundances have been normalized using ERCC internal RNA standards and corrected for filtered seawater volume, allowing for cross-sample comparison of gene expression levels. Each row represents a single transcript, annotated with multiple functional and taxonomic features (e.g., KEGG, eggNOG, Pfam, COG, GO terms, enzyme classifications, and ecotype assignments).

metaG.reference.hit_counts.by_sample.tsv

Raw gene-level read count data read-per-billion (RPB) values from metagenomic samples collected during high-resolution vertical surveys around the deep chlorophyll maximum (DCM) in cyclonic and anticyclonic eddies during the MESO-SCOPE cruise. Each row corresponds to a specific gene contig (e.g., MSD00-20a-VH-SL2C02-0123__DCM__c281_1), and each column corresponds to a unique metagenomic sample ID from around the DCM layer.

Supplementary tables Sheyn et al.xlsx

Supplementary data supporting the analyses presented in the manuscript “Mesoscale eddies shape Prochlorococcus population dynamics in the open ocean.” Each sheet provides processed results from amplicon, metagenomic, and metatranscriptomic datasets collected during the 2017 MESO-SCOPE cruise in the North Pacific Subtropical Gyre. 

MetaG.Vertical.hiRes.samples.log

Metadata for high-resolution metagenomic samples collected during the 2017 MESO-SCOPE cruise.

Each row in this dataset represents a unique vertical profile seawater sample collected during cast deployments at Station 15 (frontal region), Station 16 (SL1, cyclone), and Station 17 (SL2, anticyclone). Samples were collected at fine-scale 5-meter intervals across the water column and include associated environmental metadata such as chlorophyll concentration, dissolved oxygen, salinity, temperature, pressure, and nutrients (e.g., phosphate). Sample identifiers (e.g., MS00-20a-VHR-S15C3-A05) encode the cruise ID, sampling type (VHR: Vertical High Resolution), station number, cast number, and depth tier. Deep chlorophyll maximum (DCM) samples are specifically indicated in the sample_name column. This metadata supports high-resolution analyses of microbial community structure and function along environmental gradients.

Additional Related Data

16S rRNA gene amplicon sequences from the MESO-SCOPE (KM1709) and HOE-Legacy 4 (KOK1607) cruises are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596510 and https://www.ncbi.nlm.nih.gov/bioproject/707586, respectively.

Cloned 16S rRNA-ITS-23S rRNAs from the MESO-SCOPE (KM1709) cruise are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596510.

Metagenome depth profiles in the eddies from the MESO-SCOPE (KM1709) cruise are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596510.

Metatranscriptomes from 15 m and the DCM in the eddies from the MESO-SCOPE (KM1709) cruise are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596510.

MESO-SCOPE (KM1709) environmental metadata are available at http://scope.soest.hawaii.edu/data/mesoscope/mesoscope.html.

HOE-Legacy 4 (KOK1607) environmental metadata are available at http://scope.soest.hawaii.edu/data/hoelegacy/documents.