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.
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.
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.
Project description:This dataset consists of 20 metaproteomic analyses of the Western Atlantic Ocean aboard the R/V Knorr KN210-04 DeepDOM expedition in 2013. Samples were collected by McLane pumps on GFF or GF75 filters, split, and frozen until analyses. Expedition metadata and co-sampled datasets are available at: https://www.bco-dmo.org/deployment/59057
