Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
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| log in | [Diatom Pfam differential expression data] - Pfam differential expression data for diatoms from an iron incubation experiment during the PUPCYCLE II R/V Sally Ride cruise within the California Current System in May and June of 2023 (CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans) | This dataset includes RNA-seq differential expression results of Pfam domains within diatoms from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise with Chief Scientist Adrian Marchetti. PUPCYCLE II (Phytoplankton response to the UPwelling CYCLE) took place onboard the R/V Sally Ride from May 29th to June 10th, 2023. Freshly upwelled seawater for the incubation experiment was collected within the northern CCS and placed into designated cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (Ctrl), nine were amended with 5 nM FeCl2 (+Fe), and nine were amended with 200 nM Desferrioxamine B, a strong iron chelator (DFB). Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation. Approximately 2.5 to 4 liters of each sample was harvested for RNA-seq of the natural phytoplankton community, or metatranscriptomics. The dataset provides differential expression results of Pfam domains within diatoms (and which genera they map to), specifically comparing expression levels between +Fe and DFB at T1 and T2. These data include domains that significantly differ in expression between treatments in diatoms, and results were used to compare how strict phototrophs like diatoms transcriptionally respond to iron bioavailability compared to mixotrophs.\n\ncdm_data_type = Other\nVARIABLES:\nTaxa_Group (unitless)\nTimepoint (unitless)\nDE_Comparison (unitless)\nPfam_ID (unitless)\nPfam_Name (unitless)\nPfam_Description (unitless)\nbaseMean (number of normalized reads)\nlog2FoldChange (unitless)\nlfcSE (unitless)\nstat (unitless)\npvalue (unitless)\n... (55 more variables)\n | BCO-DMO | bcodmo_dataset_1004674_v1 | ||||||||||||
| log in | [Mixotroph Pfam differential expression (PUPCYCLE II)] - Pfam differential expression data for mixotrophs from an iron incubation experiment during the PUPCYCLE II R/V Sally Ride cruise within the California Current System in May and June of 2023 (CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans) | This dataset includes RNA-seq differential expression results of Pfam domains within mixotrophs from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise with Chief Scientist Adrian Marchetti. PUPCYCLE II (Phytoplankton response to the UPwelling CYCLE) took place onboard the R/V Sally Ride from May 29th to June 10th, 2023. Freshly upwelled seawater for the incubation experiment was collected within the northern CCS and placed into designated cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (Ctrl), nine were amended with 5 nM FeCl2 (+Fe), and nine were amended with 200 nM Desferrioxamine B, a strong iron chelator (DFB). Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation. Approximately 2.5 to 4 liters of each sample was harvested for RNA-seq of the natural phytoplankton community, or metatranscriptomics. The dataset provides differential expression results of Pfam domains within mixotrophs (and which genera they map to), specifically comparing expression levels between +Fe and DFB at T1 and T2. This data includes domains that significantly differ in expression between treatments in mixotrophs, and results were used to understand phagotrophic versus phototrophic gene expression based on iron bioavailability.\n\ncdm_data_type = Other\nVARIABLES:\nTaxa_Group (unitless)\nTimepoint (unitless)\nDE_Comparison (unitless)\nPfam_ID (unitless)\nPfam_Name (unitless)\nPfam_Description (unitless)\nbaseMean (number of normalized reads)\nlog2FoldChange (unitless)\nlfcSE (unitless)\nstat (unitless)\npvalue (unitless)\n... (38 more variables)\n | BCO-DMO | bcodmo_dataset_1004659_v1 |