Ontology highlight
ABSTRACT:
PROVIDER: PRJNA815969 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18323978.fastq.gz | Fastqsanger.gz | |||
| SRR18323979.fastq.gz | Fastqsanger.gz | |||
| SRR18323980_1.fastq.gz | Fastqsanger.gz | |||
| SRR18323980_2.fastq.gz | Fastqsanger.gz | |||
| SRR18323981_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows. Experiment, Yellow nose vs. Black nose HanWoo
2013-12-26 | E-GEOD-53657 | biostudies-arrayexpress
Project description:The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows.
2013-12-26 | GSE53657 | GEO
Project description:The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, population-specific genetic variants with moderate effects were identified, particularly in loci associated with traits underlying body size and behavioral variations, potentially explaining the observed phenotypic diversity based on coat colors. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations that were previously inaccessible.
2024-04-05 | E-MTAB-13939 | biostudies-arrayexpress
Project description:To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.
2015-12-31 | GSE63389 | GEO
Project description:The aim of this study was to investigate whether long term intake of pea fiber would improve colonic barrier, bacterial profile and alter colonic gene expression using DNA microarray. Fifty weaned pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of pea fiber from weaning age until d 160. The two diets had similar nutrient levels. Pigs fed pea fiber diet (PF diet) had markedly decreased overall average daily feed intake (ADFI) and Feed:Gain in growing and finishing period (P<0.05). In addition, long term intake of PF diet induced deeper crypt (+50 %, P<0.05), increased protein expression of colonic mucin and sIgA (+13～16 %, P<0.05). Resulting from the increased lactobacillus content (P<0.05), moreover, pigs fed PF diet had significantly higher concentration of colonic total short chain fatty acid (SCFA) and acetic acid. DNA microarray results indicated that feeding PF diet induced alterations in the expression of colonic cancer, immune response and lipid metabolism-related genes, as well as genes involved in signal pathway such as intestinal immune network for IgA production, PPAR signaling pathway and nutrient metabolism-related pathways. Collectively, our results suggested that long term intake of PF diet would improve colonic health via altering colonic bacteria profile, colonic barriers, immune and metabolism related protein or gene expressions. A total of 50 weaned pigs (Duroc×Landrace×Yorkshire, initial body weight: 7.2±0.5 kg) were randomly allocated to 2 groups with 5 pens each group and 5 pig each pen. Pigs were fed control (Control) and fibrous diets (10～20 % inclusion of pea fiber, PF) from weaning at 28 day to 160 day-old-age, which is subjected to phase feeding by weaning diet (weaning to d 30 post-weaning), growing diet (d 30～90 postweaning) and finishing diet (d 90～160 postweaning) according to their physiological stage. At d 160 postweaning, four pigs each group were selected to be slaughtered for collection of colonic tissues and DNA microarray was applied to the colonic tissues for analysis of gene expression.
2013-01-30 | E-GEOD-43917 | biostudies-arrayexpress
Project description:We combined an experimental microbiome of 11 bacterial strains isolated from the gut of native Caenorhabditis elegans. C. elegans were maintained on the experimental microbiome, Escherichia coli OP50 (control food source), or OP50 supplemented with cell-free media (CFM) from the experimental microbiome. For each of the three feeding conditions, RNA-seq was performed for wildtype (N2) worms or transgenic worms expressing amyloid beta 1-42 in their body wall muscle (GMC101).
2022-06-23 | E-MTAB-10693 | biostudies-arrayexpress
Project description:Leber2015 - Mucosal immunity and gut
microbiome interaction during C. difficile infection
This model is described in the article:
Systems Modeling of
Interactions between Mucosal Immunity and the Gut Microbiome
during Clostridium difficile Infection.
Leber A, Viladomiu M, Hontecillas R,
Abedi V, Philipson C, Hoops S, Howard B, Bassaganya-Riera
J.
PLoS ONE 2015; 10(7): e0134849
Abstract:
Clostridium difficile infections are associated with the use
of broad-spectrum antibiotics and result in an exuberant
inflammatory response, leading to nosocomial diarrhea, colitis
and even death. To better understand the dynamics of mucosal
immunity during C. difficile infection from initiation through
expansion to resolution, we built a computational model of the
mucosal immune response to the bacterium. The model was
calibrated using data from a mouse model of C. difficile
infection. The model demonstrates a crucial role of T helper 17
(Th17) effector responses in the colonic lamina propria and
luminal commensal bacteria populations in the clearance of C.
difficile and colonic pathology, whereas regulatory T (Treg)
cells responses are associated with the recovery phase. In
addition, the production of anti-microbial peptides by inflamed
epithelial cells and activated neutrophils in response to C.
difficile infection inhibit the re-growth of beneficial
commensal bacterial species. Computational simulations suggest
that the removal of neutrophil and epithelial cell derived
anti-microbial inhibitions, separately and together, on
commensal bacterial regrowth promote recovery and minimize
colonic inflammatory pathology. Simulation results predict a
decrease in colonic inflammatory markers, such as neutrophilic
influx and Th17 cells in the colonic lamina propria, and length
of infection with accelerated commensal bacteria re-growth
through altered anti-microbial inhibition. Computational
modeling provides novel insights on the therapeutic value of
repopulating the colonic microbiome and inducing regulatory
mucosal immune responses during C. difficile infection. Thus,
modeling mucosal immunity-gut microbiota interactions has the
potential to guide the development of targeted fecal
transplantation therapies in the context of precision medicine
interventions.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000583.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000583 | BioModels