Ontology highlight
ABSTRACT:
PROVIDER: PRJNA816617 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In the present study, the eggs of Chinese pond turtles (Mauremys reevesii) were incubated at three temperatures (26℃, 29℃ and 32℃). During the thermosensitive period (TSP) of incubation, the adrenal-kidney-gonad (AKG) complexes were sampled, and the transcriptome differences of the AKG samples were investigated using next-generation sequencing, then candidate genes associated with temperature-dependent sex determination of Reeves' Turtle were identified.
2022-04-01 | GSE98234 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
2021-08-17 | GSE181974 | GEO
Project description:Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment. Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform. Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed. A majority of DEGs were enriched in innate immune-related GO terms and pathways, such as activation of innate immune response, inflammatory response, innate immune response, NAD+ADP-ribosyltransferase activity and NAD biosynthetic process in sub-categories of GO terms, and RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, Phagosome, Jak-STAT signaling pathway in KEGG enrichment pathways. Meanwhile, several immune-related metabolic pathways were also identified including metabolism of Xenobiotics by cytochrome P450, Glutathione metabolism, Nicotinate and nicotinamide metabolism. Additionally, 15 DEGs were selected and validated their expression level by qRT-PCR to confirm accuracy of the RNA-seq. Conclusions: Our study is the first time to clarify the skin innate immunity difference between wild-type and yellow mutant rainbow trout in the natural flowing water pond culture environment. Our results show that the expression of most immune-related genes in the corresponding pathways were up-regulated in WR_S rainbow trout. We presumed that the disease resistance of WR_S rainbow trout might be stronger than YR_S rainbow trout.
2020-07-09 | GSE153997 | GEO
Project description:In recent years, the scale culture of Chinese soft-shelled turtle has developed rapidly. However, diseases in aquaculture are the main problems affecting the rapid and healthy cultivation. Strengthening the immunity of Chinese soft-shelled turtles is extremely important to control the infection of pathogenic bacteria. Bacillus has attracted attention as a probiotic supplement in aquatic feeds.In our previous studies, we found that the addition of Bacillus subtilis B10 to diets could increase survival rate, daily weight gain (DG) and feed conversion ratio (FCR) of Chinese soft-shelled turtles, improving the activities of digestive enzyme and optimizing the microbial communities of intestinal in Chinese soft-shelled turtle.However, the study on the mechanism of Bacillus subtilis B10 in Chinese soft-shelled turtle culture remains rare. Therefore, in this study, we used Bacillus subtilis B10 to feed the turtle, and used RNA-seq to explore its mechanism.
2022-09-01 | GSE183769 | GEO
Project description:Differential DNA methylation is characteristic of gene regulatory regions, such as enhancers, which mostly constitute low or intermediate CpG content in their DNA sequence. Consequently, quantification of changes in DNA methylation at these sites is challenging. Given DNA methylation across most of the mammalian genome is maintained, use of genome-wide bisulfite sequencing to measure fractional changes in DNA methylation at specific sites is an overexertion which is both expensive and cumbersome. Here we developed a MethylRAD technique with an improved experimental plan and bioinformatic analysis tool to examine regional DNA methylation changes in embryonic stem cells (ESCs) during differentiation. The transcriptional silencing of pluripotency genes (PpGs) during ESC differentiation is accompanied by PpG enhancer (PpGe) silencing mediated by demethylation of H3K4me1 by LSD1. Our MethylRAD data show that in presence of LSD1 inhibitor, a significant fraction of LSD1-bound PpGe fails to gain DNA methylation. We further show that this effect is mostly observed at PpGe with low/intermediate CpG content. Underscoring the sensitivity and accuracy of MethylRAD sequencing, our study demonstrates that this method can detect small changes in DNA methylation at regulatory regions including with low/intermediate CpG content, thus asserting it use as a method of choice for diagnostic purpose.
2021-04-08 | GSE158587 | GEO
Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments.
2013-05-22 | GSE41240 | GEO
Project description:ATAC-seq analysis of human CD8 T cells specific for the NS4B-214 epitope in the Yellow fever vaccine YFV-17D strain
2017-12-13 | GSE101609 | GEO
Project description:Arabidopsis thaliana MethylRAD sequencing
| PRJNA260326 | ENA