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C-CoMP Data Contributions

The following tables provide information about C-CoMP data and code contributions. This is a running list that is updated regularly. A merged copy is available for download from Zenodo (10.5281/zenodo.16615841).

C-CoMP Contributions: 26 to 70

C-CoMP Pub #Accession/linkRepository/platformData typeDescriptionPublication
028 and 041PRJNA769790NCBI Sequence Read Archive18S rRNA amplicon sequencesBIOS-SCOPE program cast profile raw amplicon sequencing data (including 18S rRNA sequences and phages from cruise AE1712)Anderson et al. 2024 and Warwick-Dugdale et al. 2024
028BATS-parasitesGithubMixedContains QIIME 2 compatible files, metadata tables, network files (Cytoscape), and R code needed to perform data analysis for Anderson et al. 2024Anderson et al. 2024
030PRJNA787291NCBI Sequence Read ArchiveTranscriptomicsRaw transcript sequences from Micromonas commoda RCC 299 accompanying Hamilton et al. 2024Hamilton et al. 2024
03010.5281/zenodo.5822680ZenodoMixedFiles for the co-culture transcript expression of Micromonas commoda RCC299 with Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, or Polaribacter sp. MED152Hamilton et al. 2024
032MTBLS567MetaboLightsMS MetabolomicsIntracellular and extracellular metabolites from three strains of ProchlorococcusKujawinski et al. 2023
032Pro_mtabsGithubCodeCode for finding KEGG compound information for Prochlorococcus strainsKujawinski et al. 2023
03410.5281/zenodo.10794740ZenodoMixedSupplementary datasets for Howard-Varona et al. 2024Howard-Varona et al. 2024
036PXD031524PRIDEMixedP. antarctica CCMP1871 mass spectrometry culture proteomics data and transcriptome-derived FASTA filesRao et al. 2024
036Phaeo-Fe-B12GithubCodeCode for statistical analysis accompanying Rao et al. 2024Rao et al. 2024
039MASSGithubCodeCodebase for Herbst et al. 2024Herbst et al. 2024
040PRJNA1234665NCBI Sequence Read Archive16S rRNA amplicon sequences16S rRNA raw amplicon sequences (amplified using primers 515F-Y/926R) from the competition assays in Clerc et al. 2025Clerc et al. 2025
04010.5281/zenodo.12210967ZenodoCodeComputational notebook demonstrating Monte Carlo uncertainty calculations for Clerc et al. 2025Clerc et al. 2025
041AE1712-viromesGithubCodeAnalysis code accompanying Warwick-Dugdale et al. 2024Warwick-Dugdale et al. 2024
0422023-anvio-comparisonGithubCodeSnakemake workflow is used to run the main analysis and generation of the files for Kananen et al. 2025Kananen et al. 2025
044PRJNA1074799NCBI Sequence Read Archive16S rRNA amplicon sequencesRaw 16S rRNA sequences accompanying Silverstein et al. 2024Silverstein et al. 2024
044MetabolicComplexityDivergenceGithubMixedProcessed data and analysis and simulation code accompanying Silverstein et al. 2024Silverstein et al. 2024
054Alteromonas_mtab_uptakeGithubMixedCode and data for the analysis of experiments testing the relationship between Alteromonas macleodii MIT1002 and select Prochlorococcus metabolites.Halloran et al. 2025 preprint
057Dukovski_et_al_2024GithubMixedReproducible workflow for Dukovski et al. 2024 preprint, including computational input files, models, layouts and scriptsDukovski et al. 2024 preprint
061GSE264347Gene Expression OmnibusTranscriptomicsTranscripts from Prochlorococcus marinus str. NATL2A and Alteromonas macleodii for parental and dark-tolerant cell lines every 4-5h over a full 13:11 light:dark cycleCoe et al. 2024
065SAR11_metabolismGithubMixedReproducible workflow (including code and necessary input/output files) that accompanies Tucker et al. 2025 preprintTucker et al. 2025 preprint
06910.5281/zenodo.15336746ZenodoProteomicsProcessed metalloproteomic metal and protein data accompanying Saito and McIlvin et al. 2025 preprintSaito and McIlvin et al. 2025 preprint
069Metalloproteomic-ViewerGithubCodeThe Jupyter notebook code for data analysis and visualization accompanying Saito and McIlvin et al. 2025 preprintSaito and McIlvin et al. 2025 preprint
06910.5281/zenodo.15336754ZenodoGenomeGenome of Pseudomonas aeruginosa strain 1-54 available as a .fasta fileSaito and McIlvin et al. 2025 preprint
07010.6084/m9.figshare.28208018FigshareFilesFiles for reproducible workflow that accompanies Schechter et al. 2025 preprintSchechter et al. 2025 preprint
070https://merenlab.org/data/ecophylo-ribosomal-proteins/WebpageCodeReproducible workflow that accompanies Schechter et al. 2025 preprintSchechter et al. 2025 preprint
Not assigned875600BCO-DMOProteomicsProcessed spectral counts of identified proteins from the proteome of Ruergeria pomeroyi DSS-3Unpublished manuscript
Not assignedPXD034365PRIDEProteomicsRaw proteomics data from Ruergeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 that accompany BCO-DMO datasets 875600 and 875612Unpublished manuscript
Not assigned875612BCO-DMOProteomicsProcessed spectral counts of identified proteins from the proteome of Alteromas macleodii MIT1002Unpublished manuscript
Not assigned927507BCO-DMOProteomicsNormalized protein abundance data and protein annotations for proteomic data from laboratory cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture mediaUnpublished manuscript
Not assignedPXD045824PRIDEProteomicsRaw proteomics data from laboratory cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substratesUnpublished manuscript
Not assigned916134BCO-DMOTranscriptomicsMetadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substratesUnpublished manuscript
Not assignedPRJNA972985NCBI Sequence Read ArchiveTranscriptomicsRaw transcript sequences from Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 that were grown in defined minimal media with specific organic substrates (with either glucose, acetate, or a mix of both as carbon substrates)Unpublished manuscript
Not assigned875622BCO-DMOProteomicsMetadata for metaproteomic samples taken from Station 2 from R/V Knorr KN210-04 in the Western Atlantic Ocean between Uruguay and Barbados from March 2013Unpublished manuscript
Not assignedPXD034035PRIDEProteomicsRaw proteomics data from Station 2 from R/V Knorr KN210-04 in the Western Atlantic Ocean between Uruguay and Barbados from March 2013 that accompany BCO-DMO dataset 875622Unpublished manuscript
Not assigned963210BCO-DMOMulti 'omicsDiel multi 'omics metadata from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021Tucker et al. unpublished manuscript
Not assignedPRJNA1201851NCBI Sequence Read ArchiveMulti 'omicsRaw sequence reads from a multi 'omics dataset (short-read and long-read metagenomes, metatranscriptomes, transfer RNA (tRNA) transcripts) collected every 90 minutes for 48 hours at two stations located in the coastal and the adjacent offshore tropical PacificTucker et al. unpublished manuscript
Not assigned10.6084/m9.figshare.28784717FigshareMetagenomic assembliesAnvi'o contigs-db files for the indivdiual co-assemblies of short-read (SR) as well as long-read (LR) sequencing of HADS metagenomesTucker et al. unpublished manuscript
Not assigned10.6084/m9.figshare.28784762FigshareMetagenomic assembliesFASTA files for metagenome-assembled genomes (MAGs) reconstructed from short-read and long-read sequencing of the metagenomesTucker et al. unpublished manuscript
Not assigned10.6084/m9.figshare.28784765FigshareAnalysis filesEcoPhylo output that describes the phylogeography of ribosomal protein L14Tucker et al. unpublished manuscript
Not assignedPRJNA1235278NCBI Sequence Read ArchiveMetagenomic assemblieshigh-quality assembled genomes (MAGs) from the Hawaiʻi Diel Sampling (HaDS) short-read metagenomesTucker et al. unpublished manuscript
Not assignedDiel Multi Omics From the Hawaii Diel Sampling (HaDS)CMAPMIxedBiogeochemical measurements, sample IDs, and sequence file information for the Hawaiʻi Diel Sampling (HaDS) projectTucker et al. unpublished manuscript
Not assigned962727BCO-DMOCell concentrationsCell concentrations associated with genomics sampling to characterize bacterial responses to parasite-host metabolites from bottle incubation experiments in June of 2024. Includes processed, raw .xml and .fcs filesAnderson et al. unpublished manuscript
Not assigned962736BCO-DMOCell concentrations and DOC concentrationsCell concentrations, percent of host infected, and bulk dissolved organic carbon (DOC) from laboratory experiments examining parasite-host metabolites in 2023. Includes processed, raw .xml and .fcs filesAnderson et al. unpublished manuscript
Not assigned10.5281/zenodo.15626552Zenodo16S rRNA amplicon sequences16s rRNA amplicon sequence files generated from the C-CoMP B2P BIOS Research Week 2024 exometabolite incubation experiment conducted at the Bermuda Institute of Ocean Sciences in March 2024Unpublished manuscript
Not assignedB2P23-BIOS-WeekGithubCodeCode for 16S rRNA amplicon sequence analysis from C-CoMP B2P BIOS Research Week 2024Unpublished manuscript
Not assigned10.5281/zenodo.15187187ZenodoMixedData, processed data, and code originating from the JGI project, "Inferring virus-host interactions through multi-omics high-resolution time series" to be used in BATS data product created by C-CoMPUnpublished manuscript

C-CoMP Contributions: 1 to 27

C-CoMP Pub #Accession/linkRepository/platformData typeDescriptionPublication
002PRJNA649292NCBI Sequence Read ArchiveTranscriptomicsTranscriptional responses in marine phytoplankton-bacteria model system: T. pseudonana CCMP1335 and R. pomeroyi DSS-3Uchimiya et al. 2021
002PR001019Metabolomics WorkbenchNMR metabolomicsT. pseudonana CCMP1335 endometabolomeUchimiya et al. 2021
003labile_DOC_supply_chainGithubCodeR code for the labile DOC model in Moran et al. 2022Moran et al. 2022
004PRJNA758094NCBI Sequence Read ArchiveMetatranscriptomicsMetatranscriptomics from T. pseudonana CCMP1335 co-cultures with R. pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and P. dokdonensis MED152Olofsson et al. 2022
004PR001231Metabolomics WorkbenchNMR metabolomicsT. pseudonana CCMP1335 endometabolomeOlofsson et al. 2022
00410.5281/zenodo.6344452ZenodoMixedSupplementary data (bacterial cell counts), tables, and figures accompanying to Olofsson et al. 2022Olofsson et al. 2022
005coenzymesGithubMixedData and code accompanying Goldford et al. 2022Goldford et al. 2022
00610.5281/zenodo.6569900ZenodoMixedExperimental data and code accompanying Zomorrodi et al. 2022Zomorrodi et al. 2022
007GSE94951Gene Expression OmnibusTranscriptomicsTranscripts from Trichodesmium erythraeum IMS101 in high-CO2 nutrient limitation experimentsWalworth et al. 2021
007PXD010515PRIDELC-MSMS ProteomicsProteins from Trichodesmium erythraeum IMS101 in high-CO2 nutrient limitation experimentsWalworth et al. 2021
007RNA-Protein_MATLAB_modelGithubCodeRNA-protein (transcriptome - proteome) MATLAB model to environmental stimuli and examines fold change correlationsWalworth et al. 2021
008MTBLS1544MetaboLightsNMR metabolomicsExometabolite drawdown of bacteria from Thalassiosira pseudonana as measured using NMRHolderman et al. 2022
008MTBLS1751MetaboLightsMS metabolomicsExometabolite drawdown of bacteria from Thalassiosira pseudonana as measured using UPLC-MS (mass spectrometry)Holderman et al. 2022
009marine_heterotrophsGithubMixedData and code accompanying Forchielli et al. 2022Forchielli et al. 2022
010Cyano_phage_grazer_omicsCyverseMixedGenomes, metabolomics analysis, and scripts accompanying Howard-Varona et al. 2022Howard-Varona et al. 2022
010Metabolomics_CyanophageGrazerGithubCodeMetabolomics analysis scripts accompanying Howard-Varona et al. 2022Howard-Varona et al. 2022
01210.5281/zenodo.6993508ZenodoCodeSimple, 1-dimensional NPZD model in Matlab, based on Kuhn et al. 2015, with a Graphical User InterfaceFennel et al. 2022
01210.5281/zenodo.6994739ZenodoCodeContains Jupyter notebooks demonstrating parameter optimization and state estimation techniques, applied to a zero-dimensional ocean biological modelFennel et al. 2022
01210.5281/zenodo.6974184ZenodoCodeMatlab code used to perform the deterministic formulation of the Ensemble Kalman Filter (DEnKF) in the Regional Ocean Modelling System (ROMS)Fennel et al. 2022
013mspacmamGithubCodeModel code for the Model of Sinking Particles and Cycling of Marine Aggregated Matter (MSPACMAM), a numerical 1-D modelDinauer et al. 2022
01510.5281/zenodo.7489891ZenodoCodeData and code accompanying Schreier et al. 2023Schreier et al. 2023
015PRJNA910220NCBI Sequence Read ArchiveTransposan sequencing (Tn-Seq)Raw transposan sequences from a co-culture experiment with Ruegeria pomeroyi DSS-3, Thalassiosira pseudonana CCMP 1335, and (or without) Vibrio hepatarius HF70 & Marivivens donghaensis HF1Schreier et al. 2023
01510.5281/zenodo.7489904ZenodoFileWig formatted file output from TRANSIT with all transposon insertions accompany Schreier et al. 2023Schreier et al. 2023
016PRJNA787291NCBI Sequence Read ArchiveTranscriptomicsRaw transcripts from Micromonas commoda co-cultured individually with R. pomeroyi DSS-3, Stenotrophomonas SKA14a and Polaribacter MED152Ferrer-González et al. 2023
01610.5281/zenodo.6812122ZenodoMixedData product files accompanying Ferrer-González et al. 2023Ferrer-González et al. 2023
017PR001487Metabolomics WorkbenchMixedRaw and processed NMR metabolomics data and code from Thalassiosira pseudonana using J-resolved STOCSY and INADEQUATEUchimiya et al. 2023
018PRJNA505827NCBI Sequence Read ArchiveMetagenomicsRaw metagenomic reads (marine environmental genomes and single-cell genomes) from Monterey BayNowinski et al. 2023
018756376BCO-DMOCTD dataEnvironmental data from CTD during the Fall 2016 ESP deployment in Monterey Bay, CANowinski et al. 2023
018756413BCO-DMOEnvironmental dataEnvironmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay, CANowinski et al. 2023
019NAEarth System Grid FederationModel output dataFiles containing variables for bacc: bacterial carbon biomass, dissoc: DOC, detoc: POC, and thetao: water temperatureKim et al. 2023
021co_culture_deviceGithubMixedContains code and data related to the BioMe deviceJo et al. 2023
022904246BCO-DMOMutant screening growth resultsHigh throughput growth screening of the marine bacterium Ruegeria pomeroyi DSS-3 knockout mutants on 70 environmentally relevant marine substrates done in 2021Schroer et al. 2023
022894179BCO-DMOMutant screening growth resultsHigh resolution growth screen of Ruegeria pomeroyi transporter mutants from September 2021 - June 2022Schroer et al. 2023
022893256BCO-DMOMutant RB-TnSeq screen resultsRuegeria pomeroyi RB-TnSeq transponson mutant library screen from February 2021Schroer et al. 2023
022PR001531Metabolomics WorkbenchMixedRaw and processed NMR metabolomics data and code from mutant-substrate pairs accompanying Schroer et al. 2023Schroer et al. 2023
02410.5281/zenodo.10402440ZenodoData productRuegeria pomeroyi digital microbe databasesVeseli et al. 2024
02410.5281/zenodo.10038194ZenodoData productAlteromonas spp. Digital Organism DatabasesVeseli et al. 2024
NAVeseli et al. 2024ZenodoData productAlteromonas spp. digital microbe that contains a pangenome (without singleton genes) as well as corresponding item and layer dataunpublished manuscript
024digital-microbeGithubCodeReproducible code workflows that accompany Veseli et al. 2024Veseli et al. 2024
024PXD045824PRIDEProteomicsR. pomeroyi raw proteomics data accompanying Veseli et al. 2024. Metadata and processed data available on BCO-DMO dataset 927507Veseli et al. 2024
024927507BCO-DMOMixedNormalized protein abundance data and protein annotations for proteomic data from laboratory cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 in 2022Veseli et al. 2024
024PRJNA972985NCBI Sequence Read ArchiveTranscriptomicsRaw transcripts from Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 in response to specific substrate availabilityVeseli et al. 2024
024916134BCO-DMOMetadataMetadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002Veseli et al. 2024
025vEcoliGithubCodeFull source code accompanying Skalnik et al. 2023Skalnik et al. 2023
02510.5281/zenodo.7709618ZenodoCodeThis version of the code will reproduce results reported in Skalnik et al. 2023Skalnik et al. 2023
02510.5281/zenodo.7709450ZenodoFilesData files used to create figures in Skalnik et al. 2023Skalnik et al. 2023
027MiCoNEGithubCodeCode for MiCoNE python packageKishore et al. 2023
027MiCoNE-pipeline-paperGithubMixedData and scripts for writing Kishore et al. 2023Kishore et al. 2023
027MiCoNE-synthetic-dataGithubMixedSynthetic data and generation scripts for Kishore et al. 2023Kishore et al. 2023
02710.5281/zenodo.7051556ZenodoDataSupporting data for Kishore et al. 2023Kishore et al. 2023