Transcriptomic sequencing of subcutaneous fat of Guangdong small-eared pigs (GS) and Yorkshire pigs (YK) at different ages（9d and 80d)
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE239580 | GEO | 2026/07/28
REPOSITORIES: GEO
Similar Datasets
Project description:Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. We selected Laiwu and Yorkshire pigs as models, and transcriptomic analysis was conducted on the longissimus dorsi muscle to investigate the gene expression patterns linked to high and low intramuscular fat (IMF) content. The purpose of the study was to determine the differences in intramuscular fat between the two breeds and identify the reasons for the differences. To further systematically investigate the potential biologic significance of phenotype divergence, the identified DEGs were annotated into multiple pathways based on KEGG bioinformatic databases (P < 0.05). According to the identified DEGs, the results revealed a number of enriched pathways in AMPK signaling pathway, cAMP signaling pathway, PPAR signaling pathway, and so on. Functional enrichment analysis showed that PPARγ, ADIPOQ, LEP, LIPE, SCD, FABP4 and PLIN1 were represented.
2025-04-18 | GSE268121 | GEO
Project description:Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality.
2017-05-20 | GSE99092 | GEO
Project description:RNA-seq data of endometrium from Yorkshire pigs
2020-06-16 | GSE141564 | GEO
Project description:Ewing sarcoma (ES) is the second most common pediatric malignancy of the bones and soft tissue, but few advances in therapeutic options have been made over the past several decades. A characteristic feature of ES that and an attractive therapeutic targets is the EWS-FLI1 fusion protein. A small molecule inhibitor of EWS-FLI1, YK-4-279 was as a targeted therapy option for Ewing sarcoma patients. A YK-4-279 analog, TK216, is currently in clinical trial. With any targeted therapy, there is always the risk that tumors will become resistant and stop responding to treatment. Here, we investigated resistance mechanisms to YK-4-279 (YK) by developing ES cell lines specifically resistant to YK. We found that expression of the cell surface protein CD99 was elevated in YK-resistant cells. Increased CD99 expression occurs within five days of YK treatment in vivo. When CD99 expression is reduced by shRNA, resistant cells regain sensitivity to YK but reducing CD99 expression in non-resistant cells does not affect sensitivity. Little is known about CD99 function in the context of Ewing sarcoma, but the data presented here indicates the function of CD99 is altered upon acquisition of YK resistance, and that CD99 serves a critical function in developed resistance to YK-4-279. RNA sequencing analysis yielded candidate genes that may also be involved in the YK resistance mechanism. We identified a potential modulator of CD99 function, ANO1, a member of the ANO family and a participant in membrane-bound ion channel activity. CD99 has previously been linked with membrane-associated ion channels. A functional association between the two proteins remains to be investigated.
2020-03-21 | GSE132762 | GEO
Project description:Fat is an important energy store in animals, especially pigs, because of their high fat deposition ability. In animal husbandry, fat content is closely related to animal's lean meat rate and other important economic traits. Long-chain non-coding RNA regulates numerous biological processes, including lipid metabolism. Resveratrol (RES) has been reported to have anti-obesity effects. However, it is unclear whether RES can control fat deposition in pigs by regulating the activities of long-chain non-coding RNAs (lncRNA). The aim of this study was to examine the expression of lncRNA in subcutaneous fat tissues of pigs fed RES-supplemented diet. A total of 12 Duroc × Landrace × Yorkshire hybrid pigs were randomly assigned to two diets, the control diet and the experimental diet containing 400 mg/kg RES. At the end of the study, RNA sequencing was carried out, and the results indicated the expression of lncRNA in the adipose tissues of pigs from the two groups. A total of 499 lncRNAs were identified. Eighty-two (82) differentially expressed genes, including 5 lncRNAs and 77 mRNAs, were also identified. We also observed that the lncRNAs, MSTRG.12490 and MSTRG.13223 targeted the mRNAs, THBS4 and SFPR2, respectively. Results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that the differentially expressed genes were mainly involved in adipocytokine signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway, and MAPK signaling pathway, which are associated with glycolipid metabolism.Results from this study contributes to the knowledge of the genes and pathways involved in fat metabolism in pigs and the role of RES in the diet of pigs.
2022-05-26 | GSE203574 | GEO
Project description:Hotspot mutations in the core promoter region of the telomerase reverse transcriptase (TERT) gene have been well established to associate with aggressive clinical characteristics, radioiodine refractory, tumor recurrence and mortality in thyroid cancer. Several E-twenty-six (ETS) transcription factors were reported to selectively bound to the mutant TERT promoter and activated TERT expression. In this study we aimed to investigate whether TERT promoter mutations confer sensitivity to ETS inhibitor YK-4-279 in thyroid cancer cells and whether this inhibitor could be served as a potential therapeutic agent for thyroid cancer. In vitro assays showed that YK-4-279 treatment sharply suppressed cell viability, colony formation, migration and invasion, as well as induced cell cycle arrest and apoptosis in a panel of thyroid cancer cells. The cell viability after YK-4-279 treatment were similar between cell lines harboring mutant and wild-type TERT promoter. Furthermore, YK-4-279 treatment reduced both luciferase activity and mRNA expression of TERT independent of TERT promoter mutation status. Data from RNA-seq further revealed that YK-4-279 significantly affected biological processes including DNA replication and cell cycle. Reduced DNA helicase activity and decreased expression of several helicase genes were observed after YK-4-279 treatment. Moreover, YK-4-279 significantly inhibited tumor growth and induced apoptosis in a xenograft mice model. Thus, ETS inhibitor YK-4-279 suppressed TERT expression and conferred anti-tumor activity in a TERT promoter mutation-independent manner, and it could be a potential agent for the treatment of advanced thyroid cancers.
2021-04-06 | GSE171473 | GEO
Project description:sRNA Sequencing during Skeletal Muscle Development between Tongcheng Pigs and Yorkshire Pigs
| PRJNA292982 | ENA
Project description:Pseudomonas fluorescens YK-310
| PRJNA705218 | ENA
Project description:Background: Marketing products with added-value characteristics is a current trend in livestock production systems. Regarding meat, selection for intramuscular fat and muscular fatty acid composition is a way to improve the palatability and juiciness of meat while assuring a healthy fat content. This represents selecting animal with a different muscular metabolic profile with respect to the extended selection of lean animals. Results: The present study has analysed the muscular gene expression profiles of 68 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. Rather than upregulation of a single pathway, the main differences lied on the transcriptional levels of genes related with lipogenesis and lipolysis, revealing the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Most strikingly, several genes which enhanced fatty acid β-oxidation and favoured insulin signalling and glucose uptake were upregulated in the fattest animals, indicating that the events leading to peripheral insulin resistance in humans with increased levels of intramuscular fat and obesity do not take place in these pigs. Moreover, neither was detected the well-characterised low-grade inflammatory state observed in overweighed humans. Conclusion: As a whole, our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to fully understand how lipid deposition affects muscle physiology in pigs. 68 gluteus medius samples form 68 animals belonging to two groups of 34 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content
2010-03-07 | E-GEOD-19275 | biostudies-arrayexpress
Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types.
2010-04-22 | GSE21412 | GEO