Ontology highlight
ABSTRACT:
PROVIDER: PRJNA674406 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12975754_1.fastq.gz | Fastqsanger.gz | |||
| SRR12975754_2.fastq.gz | Fastqsanger.gz | |||
| SRR12975755_1.fastq.gz | Fastqsanger.gz | |||
| SRR12975755_2.fastq.gz | Fastqsanger.gz | |||
| SRR12975756_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Regeneration is one of the key factors affecting downy feather production. However, the signals and molecular controlling the progression of feather regeneration was poorly understood. We used a high density microarray to profile the temporal transcriptome dynamics during the regeneration periods. A total of 3540 genes expressed differentially with significant fold changes during feather regeneration. Cluster analysis revealed event specific dynamic expression of genes related to cell cycling, cell migration, cell proliferation, follicle re-growth and fiber elongation. These clusters involved functional clusters like regulation of actin cytoskeleton, focal adhesion and sphingolipid metabolism, and enriched signaling pathways like Wnt signaling pathway, MAPK pathway and TGFβ signaling pathway. In cell cycling, mainly involved genes were cyclin B3, cyclin Y. In TGFβ signaling pathway, mainly involved genes were TGFβ3, BMP7, NOG and BMP2. While Wnt5a, Wnt10a, FZD2, and FZD10 were involved in canonical Wnt/β-catenin pathway. Our study provides a comprehensive genetic blue print of diverse cellular responses during regeneraton of goose feather. The data provide an initial step towards a better understanding of molecular mechanisms underlying feather regeneration process and also suggest that signals or molecular participated in feather regeneration was quite different from the generation of hair in mammals.
2018-02-01 | GSE65852 | GEO
Project description:The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.
2019-05-02 | GSE130568 | GEO
Project description:The unique fat storage and metabolic characteristics of goose liver is an important model for studying lipid metabolism in animals or humans. In this study, RNA sequencing technology was used to obtain the liver transcriptome of Sichuan white goose with significant weight difference in the same population, and differentially expressed genes and their pathways were identified, which may help to understand the mechanism of goose weight change. In addition, the identified candidate genes may be useful for molecular breeding of geese.
2020-02-28 | GSE132921 | GEO
Project description:Feather coloration is one of the most extraordinary examples of phenotypic diversity. This diversity results both from the variation in hue as well as from the presence/absence of pigment in distinct feather regions. The mechanisms that drive presence/absence of pigmentation in feathers are not yet fully understood. Here we characterize the gene expression profiles associated with differential melanin pigmentation in Dark-eyed junco (Junco hyemalis) tails, a social feather ornament used in courtship and male-male competition. Junco tail feathers contain both white apigmented regions as well as dark melanin-pigmented regions. We compared the transcriptome-wide gene expression in developing white and dark regions of tail feathers to understand the regulatory pathways that may regulate the development of this feather ornament. We show that both white and dark feathers express melanocyte markers, indicating that white feathers contain cells capable of producing pigment. However, only dark cells express genes associated with melanin synthesis. We identify differences in expression of genes that may regulate melanocyte activation in dark feathers. Future studies should experimentally test the role of these genes in driving differences in feather pigmentation.
2023-01-08 | GSE167085 | GEO
Project description:Transcriptome profiles of skin and feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the plumulaceous and flight feathers structure. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcritpomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns.
2018-05-07 | GSE104386 | GEO
Project description:Systematic Identification of Genes Involved in Feather Regeneration in Wanxi-White Goose
| PRJNA275228 | ENA
Project description:The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major more modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze the transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered chromatin opening sites, and they are distributed around. When a key gene is perturbed, many other co-expressed genes in the same module also will be influenced. These findings suggest that these feather / scale fate specification genes form an interconnected network, and rewiring of the gene network can lead to changes of appendage phenotypes. This work shows the key hub positions of Beta catenin and retinoic acid signaling in the hierarchy of the scale / feather fate specification gene networks, opening up new possibilities to understand the control switches of multi-component organ phenotypes.
2018-10-15 | GSE111098 | GEO
Project description:Phenotypic plasticity, the ability to switch between different morphological types, plays critical roles in environmental adaptation, leading to infections, and allowing for sexual reproduction in pathogenic Candida species. Candida tropicalis, which is both an emerging human fungal pathogen and an environmental fungus, can switch between two heritable cell types termed white and opaque. In this study, we report the discovery of a novel phenotype in C. tropicalis, named the gray phenotype. Similar to Candida albicans and Candida dubliniensis, white, gray, and opaque cell types of C. tropicalis also form a tristable switching system, where gray cells are relatively small and elongated. In C. tropicalis, gray cells exhibit intermediate levels of mating competency and virulence in a mouse systemic infection model compared to the white and opaque cell types, express a set of cell type-enriched genes, and exhibit both common and species-specific biological features. The key regulators of white-opaque transitions, Wor1 and Efg1, are not required for the gray phenotype. A comparative study of the gray phenotypes in C. tropicalis, C. albicans, and C. dubliniensis provides clues to explain the species differences in terms of virulence, ecological niches, and prevalence among these three species.
2017-01-30 | GSE81514 | GEO
Project description:Epithelial appendages are the product of epithelial – mesenchymal interactions. Tissue recombination experiments showed that in general, the dermis determines the phenotype of the epithelial appendage. Chicken dorsal skin epithelium interacts with its underlying mesenchyme to form feathers beginning at E7 (H&H stage 31), while metatarsal scale epithelium interacts with its mesenchyme to form scales beginning at E9 (H&H stage 35) which stabilize around E12 (H&H stage 38). We sought to evaluate the molecular differences of tissues with different competence and inductive abilities to form feathers and scales. Chicken embryos were selected to obtain competent E7 and non-competent at E9 feather forming skin from dorsal. The competent E9 and non-competent E11 meta-tarsal scale forming skin from metatarsal were selected for examing the differences in regional specificity. Epithelium and mesenchyme from each skin were prepared separately. Samples were prepared for RNA extraction and hybridization on Affymetrix microarrays. We gathered 8 sets of samples for the analysis: undifferentiated E7 feather skin epithelium (E7fe) and mesenchyme (E7fm); differentiated E9 feather skin epithelium (E9fe) and mesenchyme (E9fm); undifferentiated E9 scale skin epithelium (E9se) and mesenchyme (E9sm); and differentiated E11 scale skin epithelium (E11se) and mesenchyme (E11sm)
2015-07-01 | E-GEOD-62882 | biostudies-arrayexpress