GEO DataSets

(Submitter supplied) The purpose of conducting transcriptome research in this project is to explore the level of inflammatory response of the graft at the site of corpus cavernosum defect and the influence of the graft on vascularization and tissue regeneration.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

15 Samples

Download data: TSV

(Submitter supplied) The success of early pregnancy depends largely on the successful implantation of the embryo. Dynamic crosstalk between embryo and mother plays a crucial role in this process, but our understanding is still limited. Here, using the pig as a model, we first comprehensively profile the single-cell transcriptome of early free embryos and corresponding maternal endometrium, identifying embryonic and matched endometrial cells with heterogeneity. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

4 Samples

Download data: MTX, TSV

(Submitter supplied) Specific gut microbiota is critically involved in metabolic diseases, including obesity. Through analysis of gut microbiota in diabetic patients and animal models, it was found that Romboutsia ilealis is closely associated with obesity. Here, our findings show that oral administration of Romboutsia ilealis significantly alleviates diet-induced obesity and metabolic dysfunction. Interestingly, this effect occurs not through modulation of food intake or energy expenditure, but by regulating lipid absorption and metabolism in the gut. more...

Organism:

Sus scrofa

Type:

Other

Platform:

GPL26351

12 Samples

Download data: TXT

(Submitter supplied) Understanding the pulmonary adaptive immune system of pigs is of importance as respiratory pathogens present a major challenge for swine producers and pigs are increasingly used to model human pulmonary diseases. Single-cell RNA sequencing (scRNAseq) has accelerated the characterization of cellular phenotypes in the pig respiratory tract under both healthy and diseased conditions. However, combining scRNAseq with recovery of paired VJ and VDJ T cell receptor (TCR) as well as heavy (IGH) and light (IGL) chains of B cell receptors (BCR) to interrogate receptor repertoires has not to our knowledge been demonstrated for pigs. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26351

48 Samples

Download data: FASTA, MTX, TSV

(Submitter supplied) Pigs were slected based on feed conversion ratio (FCR) and classified into low FCR or high FCR. Pigs were then fed a diet with etiher a standard crude protein (CP) level, or a high or low CP level.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

36 Samples

Download data: XLSX

(Submitter supplied) We characterized the single cell landscape of lung leukocytes of healthy pigs and then compared them to pigs infected with H1N1 A/California/04/2009 with or without oseltamivir antiviral therapy.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

18 Samples

Download data: MTX, TSV

(Submitter supplied) Huntington's disease (HD) is a devastating neurodegenerative disorder caused by the expansion of CAG repeats in the huntingtin (HTT) gene. Recent advances in gene editing technologies, such as CRISPR/CasRx, have opened new avenues for therapeutic interventions. In this study, we explored the efficacy of CRISPR/CasRx, which can specifically and accurately digest single-stranded RNA and down-regulate the expression of related genes, in targeting the HTT mRNA and its potential as a treatment strategy for HD. more...

Organism:

Sus scrofa; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL26351

18 Samples

Download data: TXT

(Submitter supplied) Background: Left ventricular pressure overload (LVPO) can lead to heart failure with a preserved ejection fraction (HFpEF), whereby increased LV chamber stiffness (LV Kc) is a hallmark. However, how post-transcriptional pathways, specifically microRNAs (miRs) may contribute to increased LV Kc and HFpEF progression remains unclear. This project tested the central hypothesis that the development of HFpEF secondary to a prolonged LVPO stimulus, will result in a shift in miRs that will be related to LV Kc. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

12 Samples

Download data: XLSX

(Submitter supplied) Here, we examined the effect of LDN-193189, an inhibitor of the BMP signaling pathway, on pig embryonic stem cells (ESCs) in the absence of feeder cells to develop a feeder-free culture system. Feeder cells play an important role in supporting the pluripotency of pig ESCs by blocking trophoblast and mesodermal differentiation through inhibition of the BMP pathway. Transcriptome analysis revealed that LDN-193189 treatment instead of coculturing with feeder cells could help maintain the pluripotency and homogenous cell population of pig ESCs by stimulating the secretion of chemokines and suppressing differentiation. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

3 Samples

Download data: MTX, TSV

(Submitter supplied) To analyze gene expression profiles at the single-cell level in pigs infected with PRRSV (Porcine Reproductive and Respiratory Syndrome Virus), aiming to understand the dynamic changes in gene expression, immune responses, and cellular interactions during PRRSV infection, and identify potential targets for intervention or prevention

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

36 Samples

Download data: MTX, TSV

(Submitter supplied) Developing cost-effective and disease-relevant animal models is essential for advancing biomedical research into human disorders. This study investigates the feasibility of a pig model for autism spectrum disorder (ASD) using embryonic exposure to valproic acid (VPA), an antiepileptic drug known to increase ASD risk. We established experimental paradigms to assess the behavioral characteristics of these pig models. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

6 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) 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) 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) 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) 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

(Submitter supplied) Damage to the development of porcine gametes and embryos caused by high temperatures (HT) is one of the main reasons for the decline in the economic benefits of the livestock industry. Zygotic genome activation (ZGA) marks the beginning of gene expression programs in mammalian pre-implantation embryos. In pigs, ZGA occurs at the 4-cell (4C) stage, indicating that correct gene expression at this stage plays an important regulatory role in embryonic development. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

6 Samples

Download data: TXT