Barcode Extension for Analysis and Reconstruction of Structures (BEARS)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB18731 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: Not available
| S-EPMC5355802 | biostudies-literature
Project description:We developed a hybrid-sequencing workflow, combining next-generation and third-generation sequencing, to reconstruct full-length transcriptomes. Integrating with polysome profiling and ribosome footprinting data, we predicted isoform–specific translational status and reconstructed ORFeome. Moreover, we identified isoforms with specific subcellular localization pattern in neurons.
2019-10-14 | GSE128136 | GEO
Project description:Environmental Genomics of Late Pleistocene Black Bears and Giant Short-Faced Bears - fossils
| PRJEB44161 | ENA
Project description:Hibernating American black bears have significantly different clotting parameters than their active summer counterparts, affording them innate protection against venous thromboembolism (VTE) despite prolonged periods of immobility. Physiologic changes that occur during hibernation are thought to result from differential gene expression, rather than novel genes, and there is increasing evidence miRNAs may play an important role this regulation. We propose that significant differences exist in miRNA expression in the plasma of hibernating black bears compared to their active counter parts (summer), which lead to critical gene regulation responsible for auto-anticoagulation during hibernation. Methods: Blood was collected from 21 American black bears in the Northern Michigan Peninsula in summer 2017 and winter 2018 (11 active, 10 hibernating). Plasma was extracted Results: Fifteen miRNAs were differentially expressed in the plasma of hibernating black bears. Nine miRNAs were significantly downregulated (miR10b-3p, miR-136-3p, miR-181c-5p , miR-200a-3p, miR-200b-5p, miR-200c-3p, miR-320b, miR-320c and miR-320d) and six miRNAs were significantly upregulated (miR-15a-5p, miR-15b-3p, miR-15b-5p, miR-16-5p, miR-92a-3p, miR-150-5p) during hibernation. Twelve miRNAs had no identifiable targets, but miR-200a-3p, miR-200b-5p and miR-200c-3p found to be targets of SERPINC1, the gene responsible for the production of antithrombin (AT). Conclusions: Several miRNAs were differentially expressed in hibernating bears (12). Most importantly miR-200a-3p, miR-200b-5p and miR-200c-3p were all downregulated in hibernation and associated with increased expression of SERPINC1 and production of AT. AT is a powerful anticoagulant and this finding may explain the hibernating black bears ability to achieve auto-anticoagulation and protection from VTE.
2020-09-01 | GSE124398 | GEO
Project description:We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation in comparison to animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. The Gene Ontology and Gene Set Enrichment analysis consistently showed a highly significant enrichment of the protein biosynthesis category by over-expressed genes in both liver and skeletal muscle during hibernation. Coordinated induction in transcriptional level of genes involved in protein biosynthesis is a distinctive feature of the transcriptome in hibernating black bears. This finding implies induction of translation and suggests an adaptive mechanism that contributes to a unique ability to reduce muscle atrophy over prolonged periods of immobility during hibernation. Comparing expression profiles in bears to small mammalian hibernators shows a general trend during hibernation of transcriptional changes that include induction of genes involved in lipid metabolism and carbohydrate synthesis as well as depression of genes involved in the urea cycle and detoxification function in liver. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and muscle, were hybridized on a custom 3,200-gene nylon membrane microarray platform with three replicates for each gene (9.600 spots in total). Six hibernating and five summer active bears were studied in experiments with liver tissue, five hibernating and five summer active animals were tested with muscle tissue.
2009-03-09 | E-GEOD-15099 | biostudies-arrayexpress
Project description:RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on studying expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply this approach to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known genes. We identify novel biological variation in protein-coding genes, including thousands of novel 5'-start sites, 3'-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to provide a comprehensive picture of mammalian transcriptomes.
2010-05-01 | GSE20851 | GEO
Project description:Fecal microbiota of wild and captive Andean bears
| PRJEB21054 | ENA
Project description:Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. A total of 241 genes were differentially expressed (P < 0.01 and fold change > 0.5) in the ilium bone of bears between winter and summer. The Gene Ontology and Gene Set Enrichment analysis showed an elevated proportion in hibernating bears of over-expressed genes in six functional sets of genes involved in anabolic processes of tissue morphogenesis and development including skeletal development, cartilage development and bone biosynthesis. Apoptosis genes demonstrated a tendency for down regulation during hibernation. No coordinated directional changes were detected for genes involved in bone resorption, although some genes responsible for osteoclast formation and differentiation (Ostf1, Rab9a, c- Fos) were significantly under expressed in bone of hibernating bears. Elevated expression of multiple anabolic genes without induction of bone resorption genes, and the down regulation of apoptosis related genes, likely contribute to the adaptive mechanism that preserves bone mass and structure through prolonged periods of immobility during hibernation. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Bone RNA were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in this experiments.
2012-02-15 | E-GEOD-35796 | biostudies-arrayexpress
Project description:Here we provide mass-spectrometry based plasma proteomics data of hibernating and active wild Scandinavian brown bears (Ursus arctos arctos). The brown bear hibernates for half the year. Despite obesity and the prolonged period of inactivity, bears show no signs of the harmful effects associated with these conditions in humans. Thus, the hibernating bear is a protentional translational model for addressing these complications in humans. We analyzed plasma samples from 14 subadult 2- to 3-year-old (y/o) bears (6 males and 8 females) collected both during hibernation and active state, and for some for the bears during two seasons, resulting in a total of 38 analyzed plasma samples. In triplicates, the proteins in the plasma samples were unfolded and reduced. To increase depth of the analysis and the chance to detect low molecular weight proteins and peptides, we filtered samples with a 50K MWCO filter with the aim to deplete larger proteins. The proteins in the permeate were then tryptically digested, desalted, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein identification and quantification was performed with the MaxQuant software searching against an Ursus arctos horribilis protein database.
2021-12-21 | PXD030482 | Pride
Project description:Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. A total of 241 genes were differentially expressed (P < 0.01 and fold change > 0.5) in the ilium bone of bears between winter and summer. The Gene Ontology and Gene Set Enrichment analysis showed an elevated proportion in hibernating bears of over-expressed genes in six functional sets of genes involved in anabolic processes of tissue morphogenesis and development including skeletal development, cartilage development and bone biosynthesis. Apoptosis genes demonstrated a tendency for down regulation during hibernation. No coordinated directional changes were detected for genes involved in bone resorption, although some genes responsible for osteoclast formation and differentiation (Ostf1, Rab9a, c- Fos) were significantly under expressed in bone of hibernating bears. Elevated expression of multiple anabolic genes without induction of bone resorption genes, and the down regulation of apoptosis related genes, likely contribute to the adaptive mechanism that preserves bone mass and structure through prolonged periods of immobility during hibernation.
2012-02-15 | GSE35796 | GEO