Ontology highlight
ABSTRACT:
PROVIDER: PRJNA750518 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15365911.fastq.gz | Fastqsanger.gz | |||
| SRR15365911_1.fastq.gz | Fastqsanger.gz | |||
| SRR15365911_2.fastq.gz | Fastqsanger.gz | |||
| SRR15365912.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is nowadays widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches, and rare are the undergraduate programs offering such multi-disciplinary training. In addition, understanding the dynamic between Biology research projects and Bioinformatics analyses is challenging with no real-life experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences of the Cumming School of Medicine at the University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter of 2023 to 2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. They used Galaxy, a public web-based supercomputing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Students’ research explained the molecular mechanism behind the uncoordinated phenotype caused by the reciprocal translocation eT1(III;V) and uncovered unexpected effects on gene expression on an understudied gene. We evaluated the course’s impact on student learning journeys and showed that the CURE favored students’ understanding of the Bioinformatics field and fostered their research interest. We provide here guidelines to facilitate the CURE implementations to improve access for undergraduate students to bioinformatics research experiences.
2026-03-18 | GSE292388 | GEO
Project description:Blood plasma was collected from 9 naval aviation students 24 hours prior to and no more than 20 minutes after Modular Egress Training (psychological stressor).
2009-12-01 | PRD000158 | Pride
Project description:Gender-specific antibiotic-resistance patterns and characterization of bacterial flora of undergraduate students’ mobile phones
| PRJEB78691 | ENA
Project description:GG3 - Genome sequencing of bacteria in undergraduate classes
| PRJEB32804 | ENA
Project description:A time series from 1 hour to 9 hours post-fertilization (hpf) was collected for RNA-seq by students of the MBL Embryology Course to understand the shifts in gene expression occuring in the early embryo of Mnemiopsis leidyi.
2018-01-23 | GSE93977 | GEO
Project description:Antimicrobial-producing soil bacteria isolated by Ouachita Baptist University students
| PRJNA554317 | ENA
Project description:The interplay between microbiota and skin cells is a key factor underlying the pathophysiology of this barrier organ. Keratinocytes, the main components of the epidermis, are crucial for skin barrier function, but their responses to different bacteria are not well understood. We present a high-throughput analysis of the transcriptome of human epidermal-like organoids exposed to two vastly different bacterial skin colonists: Staphylococcus epidermidis and Staphylococcus aureus, which are commonly associated with mostly positive and negative interactions with the host, respectively. We observed partly overlapping but predominantly divergent epidermal changes in response to both bacteria. Among the genes most affected by S. aureus, those related to lipid metabolism were predominant. This work was supported by grants from the Polish National Science Center (UMO-2014/12/W/NZ6/00454 and 2019/35/B/NZ6/03357) and by a grant for research projects for Young Scientists and PhD students from the Jagiellonian University (N19/MNS/000020). The open-access publication has been supported by the Faculty of Biochemistry, Biophysics and Biotechnology under the Strategic Programme Excellence Initiative at Jagiellonian University in Krakow, Poland.
2025-03-13 | GSE276844 | GEO
Project description:To better understand the impact of infection on oocyte quality we employed global transcriptomics of oocytes collected from heifers after receiving intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes. We hypothesized that oocyte transcriptome would be altered in response to intrauterine infection. A total of 452 differentially expressed genes were identified in oocytes collected from heifers 4 days after bacteria infusion compared to vehicle infusion, while 539 differentially expressed genes were identified in oocytes collected from heifers 60 days after bacteria infusion. Only 42 genes were differentially expressed in bacteria infused heifers at both day 4 and day 60. Interferon, HMGB1, ILK, IL-6 and TGF-beta signaling pathways were downregulated in oocytes collected at day 4 from bacteria infused heifers, while interferon, ILK and IL-6 signaling were upregulated in oocytes collected at day 60 from bacteria infused heifers. These data suggest that bacterial infusion alters the oocyte transcriptome differently at day 4 and day 60, suggesting different follicle stages are susceptible to damage. Characterizing the long-term impacts of uterine infection on oocyte transcriptome aids in our understanding of how infection causes infertility in dairy cattle.
2020-01-01 | GSE141307 | GEO