Colonic Content Samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA548036 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9277300_1.fastq.gz | Fastqsanger.gz | |||
| SRR9277300_2.fastq.gz | Fastqsanger.gz | |||
| SRR9277310_1.fastq.gz | Fastqsanger.gz | |||
| SRR9277310_2.fastq.gz | Fastqsanger.gz | |||
| SRR9277320_1.fastq.gz | Fastqsanger.gz |
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Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.
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Project description:Background/ Aim: Diabetes has substantive co-occurrence with disorders of gut-brain interactions (DGBIs). The pathophysiological and molecular mechanisms linking diabetes and DGBIs are unclear. miRNAs are key regulators of diabetes and gut dysmotility. We investigated whether impaired gut barrier function regulated by a key miRNA, miR-10b-5p, links diabetes and gut dysmotility. Methods: We created a new mouse line using the Mb3Cas12a/Mb3Cpf1 endonuclease to knock out mir-10b globally. Loss of function studies were conducted to characterize diabetes, gut dysmotility, and gut barrier dysfunction phenotypes in these mice. Gain of function studies were conducted by injecting these mice with a miR-10b-5p mimic. Further, we performed miRNA-sequencing analysis from colonic mucosa from mir-10b KO, WT, and miR-10b-5p mimic injected mice to confirm 1) deficiency of miR-10b-5p in KO mice, and 2) restoration of miR-10b-5p expression after the mimic injection. Results: Congenital loss of mir-10b in mice led to the development of hyperglycemia, gut dysmotility, and gut barrier dysfunction. We found increased gut permeability and reduced expression of the tight junction protein Zonula occludens-1 (ZO-1), in the colon of mir-10b KO mice. We further confirmed that patients with diabetes or IBS-C, a known DGBI that is linked to leaky gut, had significantly reduced miR-10b-5p expression. Injection of a miR-10b-5p mimic in mir-10b KO mice rescued these molecular alterations and phenotypes. Conclusion: Our study uncovered a potential pathophysiologic mechanism of gut barrier dysfunction that links both the diabetes and gut dysmotility phenotypes in mice lacking miR-10b-5p. Treatment with a miR-10b-5p mimic reversed the leaky gut, diabetic, and gut dysmotility phenotypes, highlighting the translational potential of miR-10b-5p mimic.
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Project description:One of the most important determinants of meat quality is the intramuscular fat content (IMF). The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the current study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq technique allowed identifying in the samples analyzed around 10,000 of the 25,878 annotated genes. In addition to this, the 42.46% of the identified transcripts corresponded to newly predicted isoforms. The differential expression analyses revealed a total of 221 DE annotated genes and 116 DE newly isoforms. Functional analyses identified an enrichment of overexpressed genes in animals with a higher content of IMF involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC and ADIPOQ) and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB and SEMA4D) in the groups of animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. On the one hand, co-expression networks analyses revealed six lncRNAs (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1 and CIDEC. The computation of the regulatory impact factors (RIFs) revealed a total of 301 transcriptionally regulatory factors involved in the expression differences, some of them have a role in adipogenesis (ARID5B, CREB1, VDR, ATF6 and SP1) and other ones take part of myogenesis and development of skeletal muscle (ATF3, KLF11 and MYF6). The results obtained provide a relevant insight about the knowledge of the genetics mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors is proposed for a further identification of polymorphisms susceptible of integrate in a selection program.
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