GEO DataSets

(Submitter supplied) FSH is considered as the most critical regulatory factor for follicle growth and development. It is widely acknowledged that exogenous administration of FSH can effectively stimulate ovulation.However, these techniques have several drawbacks such as high cost and detrimental effects on hormone balance and embryo implantation.Sulforaphane (SFN) is a naturally occurring compound that belongs to the isothiocyanate group, which is predominant in cruciferous vegetables.Our previous research demonstrated SFN could inhibit hypoxia-evoked apoptosis in porcine GCs. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19176

9 Samples

Download data: XLS

(Submitter supplied) This study aims to use omics data to understand the genetic pathways involved in heat stress adaptation after a short and a long time exposure. Heat stress is one of the main performance limiting factors in the pig industry and its importance is expected to increase with the consequences of climate warming. Various solutions to mitigate the effects of heat stress on pig performance and welfare have been investigated, and genetic selection appears to be a potential solution. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL19893

75 Samples

Download data: TXT

(Submitter supplied) Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26351

20 Samples

Download data: BIGWIG, BW

(Submitter supplied) In this study, BS-seq technology was used to analyze the epigenomic analysis of liver tissues of Rongchang pigs at three important feeding stages. There was little difference in DNA methylation profiles among the neonatal, weaned and adult groups. However, we observed significant changes in DNA methylation in the gene body and promoter regions of metabolic and immune-related genes from neonates to adulthood. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19176

6 Samples

Download data: TXT

(Submitter supplied) Classical swine fever virus (CSFV) is an etiologic agent that causes a highly contagious disease in pigs. Laying a foundation to solve problems in its pathogenic mechanism, microarray analysis was performed to detect the gene transcriptional profiles in peripheral blood mononuclear cells (PBMC) following infection with a Chinese highly virulent CSFV strain Shimen. Three susceptible pigs were inoculated intramuscularly with a lethal dose (1.0 × 106 TCID50) of CSFV. more...

Organism:

Sus scrofa; Sus scrofa domesticus

Type:

Expression profiling by array

Platform:

GPL3533

10 Samples

Download data: CEL, CHP

(Submitter supplied) Homeostasis during the perinatal period is critical for the correct development of mammals and unbalances in the redox potential are common in this stage. Thus, enrichment of maternal diets with antioxidants may be useful to improve piglet early development. We have tested the effects of sows’ diet enrichment with different antioxidants on the piglets’ adipose tissue functioning, in comparison to a control diet with a basal antioxidant level, by studying gene expression and cellularity. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

24 Samples

Download data: XLSX

(Submitter supplied) [Background] DNA methylation plays a crucial role in regulating cell proliferation, differentiation, gene expression, and embryonic development. However, the comprehensive changes in genome-wide DNA methylation during early pregnancy in sows remain unknown. This study aimed to investigate the DNA methylation profiles and to construct an early gene pool of sows during early gestation.[Results] In this investigation, we utilized blood samples from 20 healthy sows and applied Reduced Representation Bisulfite Sequencing (RBSS) technology to systematically examine alterations in DNA methylation in sow blood during early pregnancy. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26351

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Skin is the largest barrier organ with complex structure and function. We investigated the transcriptional dynamics of pig skin during development and aging at single-cell resolution. Using single-cell RNA sequencing, we profiled the transcriptomes of 443,529 skin cells derived from 30 individuals of 10 developmental time points staged between 56 days of gestation and 7 years old. Our analysis identified the dynamic changes in the cellular transcriptional profile of eight skin cell types at different developmental stages, exhibiting time-dependent skin cell heterogeneity.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30998

30 Samples

Download data: MTX, TSV

(Submitter supplied) RNA- sequencing was performed to compare the effect of male sex category, i.e. entire males (EM), surgical castrates (SC), and immunocastrates (IC) on differential gene expression in LD and SSC muscles. Extracted RNA from 6 randomly selected animals of each sex category and muscle were pooled together and used for library preparation and sequencing. A total of 71 and 36 differentially expressed genes (DEGs) were detected in LD and SSC, respectively (|log2(fold change) >1| and -log10(q-value) <0.005). more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: CSV

(Submitter supplied) Although the role of asialoglycoprotein receptor 1 (ASGR1) in lowering lipid levels is well established, recent studies indicate that ASGR1 inhibition can cause unexpected liver damage in pigs, raising a serious issue about whether ASGR1 can be a good target for treating ASCVD. Here, we utilized the CRISPR/Cas9 system to regenerate ASGR1-knockout pigs, who displayed decreased lipid profiles without observable liver damage, which were confirmed by the lower levels of serum ALT and AST, reduced expression of inflammation markers, and normal histological morphology. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30998

6 Samples

Download data: TXT

(Submitter supplied) We used single cell RNA sequencing to investigate the heterogeneity of nasal mucosal cells in healthy piglets

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

2 Samples

Download data: MTX, TSV

(Submitter supplied) Most porcine embryonic stem cells (pESC) derived from in vitro blastocysts Still require complex media compositions and feeder layers which make difficulty to adapt their broad and routine use. We derived pESC using simplified culture media (FIW) consisting of small molecules FGF2, IWR-1, and WH-4-023 in serum-free medium. We established several pESC-FIW lines capable of single cell passaging with short cell doubling time (about 12 hours). more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

6 Samples

Download data: XLSX

(Submitter supplied) Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29847

22 Samples

Download data: XLSX

(Submitter supplied) Female and male pigs were studied. Half of the pigs were exposed to immune activation from virally-infected mothers, and half were not exposed. At 60 days of age about one third of the pigs were given metabolic distress (fasting), one third of the pigs were given immune distress (poly(I:C)), and one third of the pigs were given Saline (control).

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22475

112 Samples

Download data: CSV

(Submitter supplied) Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multi-omic approaches, such as single cell technologies, proteomics, metabolomics and the different types of imaging, is an inevitable step to overcome the need of disease model systems and towards translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

6 Samples

Download data: H5

(Submitter supplied) Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in African swine fever virus(ASFV) pathogenicity are largely unknown. Here, we analyzed the expression profile of lncRNAs and mRNAs in the ASFV-infected or uninfected PAMs by high-throughput sequencing

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26351

6 Samples

Download data: FA, GTF, XLS

(Submitter supplied) Studies on porcine induced pluripotent stem (iPS) cells served as a great reference for human clinical research due to the similarity in organ size, physiology, anatomy, and heredity between pig and human. However, the reprogramming efficiency of iPS cells was currently poor. In this study, we reported the induction of iPS cells from porcine Sertoli cells (SCs) via infecting with four separate lentiviral vectors expressing pig OCT4, SOX2, KLF4 and c-MYC. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26285

6 Samples

Download data: TXT

(Submitter supplied) Develop methods to elucidate the pig antibody repertoire using single B cell sequencing

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34588

2 Samples

Download data: CSV, H5

(Submitter supplied) Oocyte maturation refers to oocytes at the germinal vesicle stage progressing into metaphase II (MII) stage of development. Even though numerous studies have shown key genes and potential important signalling cascades, which drive the GV to MII transition, a system-wide analysis of underlying differences at gene level and especially at transcript level between the two developmental stages of the oocyte is still lacking. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20983

15 Samples

Download data: CSV, TSV

(Submitter supplied) Chloroquine (CQ) could function as a lysosomotropic inhibitor to impair the autophagy-lysosome pathway, and is widely used to treat malarial, tumor and recently COVID-19. However, the effect of CQ treatment on porcine immature Sertoli cells (iSCs) remains unclear.;Here we showed that CQ treatment reduced iSCs viability in a dose-dependent manner. CQ treatment (20µM) of iSCs for 36h could elevate oxidative stress, damage mitochondrial function and promote apoptosis. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

9 Samples

Download data: TXT