Analyses of miRNA in the ileum of diarrheic piglets caused by Clostridium perfringens type C
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ABSTRACT:
PROVIDER: PRJNA540421 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8989410.fastq.gz | Fastqsanger.gz | |||
| SRR8989420.fastq.gz | Fastqsanger.gz | |||
| SRR8989411.fastq.gz | Fastqsanger.gz | |||
| SRR8989421.fastq.gz | Fastqsanger.gz | |||
| SRR8989412.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed miRNA profiles of the ileum of piglets caused by Clostridium perfringens type C. Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x10e9 CFU per ml. Then, 5 piglets were randomly selected as the control group (IC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (IS) and resistant group (IR), respectively. Finally, ileum were collected and sequenced for miRNA. Result: 53 differentially expressed miRNAs were found. KEGG pathway analysis for target genes revealed that these miRNAs were involved in ErbB signaling pathway, MAPK signaling pathway, Jak-STAT signaling pathway and Wnt signaling pathway. The expression correlation analysis between miRNAs and target genes revealed that the expression of miR-7134-5p had negative correlation with target NFATC4, miR-500 had negative correlation with target ELK1, HSPA2 and IL7R, and miR-92b-3p had negative correlation with target CLCF1 in ileum of IR vs IS group, suggesting that miR-7134-5p targeting to NFATC4, miR-500 targeting to ELK1, HSPA2 and IL7R, and miR-92b-3p targeting to CLCF1 were probably involved in piglet resisting C. perfringens type C. Conclusions: The results will provide value resources for better understanding of the genetic basis of C. perfringens type C resistance in piglet and lays a new foundation for identifying novel markers of C. perfringens type C resistance
2022-04-24 | GSE130471 | GEO
Project description:Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed the transcriptome profiles of the spleen of piglets caused by Clostridium perfringens type Cens type C. Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for lncRNA and mRNA. Results: RNA libraries constructed from spleen of piglets caused by Clostridium perfringens type C were sequenced. A total of 1,450,292,484 clean reads were generated. Among them, 2056 novel lncRNA transcripts corresponding to 1561 lncRNA genes were identified, including 1811 intergenic lncRNAs and 245 anti-sense lncRNAs. The identified spleen lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other animal. Notably, in pairwise comparisons between the libraries of spleen tissue at the different group, a total of 247 lncRNA and 2170 mRNA were differentially expressed (P < 0.05). Function analyses indicated that these differentially expressed lncRNAs and mRNAs play roles in defensing Clostridium perfringens type C, which were enriched in immune-related biological processes, such as the antigen processing and presentation, TNF signaling pathway, NF-kappa B signaling pathway, B cell receptor signaling pathway and MAPK signaling pathway. Conclusions: This study provides the information of spleen-related lncRNAs in swine diarrhea with Clostridium perfringens type C. We also analyzed all lncRNA’s genomic feature and expression. Bioinformatic analysis indicates that some lncRNAs participated in important biological processes associated with defeasing Clostridium perfringens type C, such as antigen processing and presentation, the MHC protein complex and regulation of autophagy.
2018-11-01 | GSE105797 | GEO
Project description:Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed miRNA profiles of the spleen of piglets caused by Clostridium perfringens type C. Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for miRNA. Result: 88 differentially expressed miRNAs were found. KEGG pathway analysis for target genes revealed that these miRNAs were involved in MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, p53 signaling pathway and ECM-receptor interaction. And 4 miRNAs (miR-133b, miR-532-3p, miR-339-5p and miR-331-3p) of closely related to piglets resistance to C. perfringens type C were obtained. The expression correlation analysis between these miRNAs and target genes revealed that the expression of miR-133b and miR-532-3p had negative correlation with their target NFATC4, miR-339-5p had negative correlation with target HTRA3, and miR-339-5p and miR-331-3p had negative correlation with target TNFAIP8L2 in spleen, suggesting that miR-133b and miR-532-3p targeting to NFATC4, miR-339-5p targeting to HTRA3, and miR-339-5p and miR-331-3p targeting to TNFAIP8L2 were probably involved in piglet resisting C. perfringens type C. Conclusions:The results will provide value resources for better understanding of the genetic basis of C. perfringens type C resistance in piglet and lays a new foundation for identifying novel markers of C. perfringens type C resistance.
2020-06-04 | GSE145302 | GEO
Project description:Identification of miRNAs regulating Clostridium perfringens type C infection in the spleen of diarrheic piglets
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Project description:Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrhea piglets caused by Clostridium perfringens type C
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Project description:The transcriptome changes of the ileal mucosa in suckling piglets during early postnatal life were analysed to contribute to the knowledge of a pig’s gut development. In addition, the ileal transcriptome of suckling piglets was compared with that of age-matched weaned piglets (weaned at the age of 21 days) to elucidate the effect of weaning on the developing gut. DNA microarray was used to analyse the change of transcriptome profiles and biological pathways in porcine ileum that occurred during the developmental or the weaning process.
2015-09-30 | GSE65008 | GEO
Project description:Apple pomace dietary supplementation effects on piglets' microbiota (ileum and proximal colon)
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Project description:Laminaria digitata is a brown seaweed with prebiotic properties that has the potential to improve the response of weaned piglets to nutritional stress. However, its cell wall polysaccharides are not digested by the endogenous enzymes of monogastric animals. Alginate lyase has shown promise in degrading them under in vitro conditions. The objective of this study is to evaluate the effect of a 10% incorporation of L. digitata, and alginate lyase supplementation on the ileum proteome and metabolome, in a hypothesis generating approach. Control piglets increased the use of glucose as an enteric source of energy, demonstrated by the higher abundance of PKLR and PCK2 proteins and the lower concentration of glucose found in the tissue. Furthermore, seaweed inclusion promoted an increased abundance of proteins related with improved enterocyte structural integrity (ACTBL2, CRMP1, FLII, EML2 and MYLK), peptidase activity (NAALADL1, CAPNS1) and anti-inflammatory activity (C3), demonstrating improved intestinal function. Coherently, they lowered the abundance of apoptosis (ERN2) and proteolytic (DPP4) proteins. Alginate lyase supplementation seems to magnify the baseline effects of feeding the seaweed alone, by increasing the number of differential proteins in the same pathways, possibly as a consequence of increased intracellular nutrient release.
2023-09-29 | PXD043393 | Pride
Project description:To further study of pcv2-related diseases, we have employed whole genome microarray expression profiling as a discovery platform to identify ileal differentially expressed genes of piglets after pcv2 infection. Infected and uninfected piglets were sampled and analyzed by whole genome microarray expression profiling. The result showed 43603 differencially expressed genes in ileum after PCV2 infection. Expression of 11 genes (IL-1α, IL-1β, IL-6, IFNε, C5, C1QA, CCL4, CCL5, CCL25, CXCL9, CD163) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between samples.
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