Ontology highlight
ABSTRACT:
PROVIDER: PRJNA527344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8745171.fastq.gz | Fastqsanger.gz | |||
| SRR8745172.fastq.gz | Fastqsanger.gz | |||
| SRR8745173.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Untargeted proteomics from a 5,000 km+ transect across the central Pacific Ocean from Hawaii to Tahiti. The expedition crossed multiple biogeochemical provinces, inlcuding the oligotrophic North Pacific Subtropical Gyre, the extremety of the Eastern Tropical North Pacific Oxygen Deficient Zone, and the relatively productive equatorial region associated with upwelling. This dataset focuses on the microbial fraction (0.2-3.0 micrometer filter size) and the microbial community dynamics across these biogeochemical provinces, from the surface oceance to the mesopelagic (1,250 m depth maximum).
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Project description:In this study we explored the metabolism of unicellular eukaryotic organisms (protists) across a 4,600 km meridional transect in the central Pacific Ocean. The region contains a natural biogeochemical gradient spanning from low nitrogen, oligotrophic waters to a productive equatorial upwelling system. We used a combined geochemical and 'omic approach to characterize the metabolic strategies these organisms rely upon to adapt to changes in their chemical environment. Samples were collected using underwater pumps, capable of filtering hundreds of liters of seawater, from seven stations and 3-13 different depths spanning 20-1,900 m in the water column.
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Project description:Projected responses of ocean net primary productivity (NPP) to climate change are highly uncertain. The climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific plays a crucial role, but field measurements are insufficient to provide suitable constraints. Here we quantify two decades of nutrient limitation in the Equatorial Pacific with satellite observations. Using field nutrient addition experiments, proteomics, and above-water hyperspectral radiometry, we demonstrate that physiological responses of phytoplankton to iron limitation led to ~3-fold increases in chlorophyll-normalized phytoplankton fluorescence. Extension to the >18-year satellite fluorescence record showed that Equatorial Pacific iron limitation was robust to changes in physical forcing through multiple El Niño–Southern Oscillation cycles, despite coherent fluctuations in limitation strength. In contrast, these iron limitation changes were overestimated 2-fold by a state-of-the-art climate model. Such synoptic constraints provide a powerful new approach for benchmarking the realism of model NPP projections to climate changes.
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Project description:To define the skeletal muscle adaptations induced by exercise performed at high altitude hypoxia, we investigated if the gene expression profile of Vastus lateralis muscle was affected by 5000 m-above-sl-expedition. Two-condition experiment, Vastus lateralis muscle biopsy post-expedition vs Vastus lateralis muscle biopsy pre-expedition. Five volunteers/climbers. Biological replicates: 1 pre-expedition sample, 1 post-expedition sample.
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Project description:Alternative splicing (AS) generates isoform diversity critical for cellular identity and homeostasis, yet characterization of this diversity in single cells remains limited. We developed Expedition, a computational framework to categorize and visualize the heterogeneity of AS from single-cell transcriptomes. Expedition consists of (i) outrigger, a de novo splice graph transversal algorithm to detect AS from single cell RNA-seq; (ii) anchor, a Bayesian approach to assign splicing modalities and (iii) bonvoyage, using non-negative matrix factorization to visualize modality changes. By applying Expedition to single iPSCs undergoing neuron differentiation, we discover that 25% of AS exons exhibit bimodality and are flanked by longer and more conserved introns harboring distinct cis-regulatory motifs. Bimodal exons are highly dynamic during cellular transitions, preserve translatability, enriched in recently emerged genes and have conserved AS in mammals. Applying Expedition (http://github.com/YeoLab/Expedition) in single cells redefines our estimates and understanding of AS in evolution and biology.
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