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Relative MicroRNA expresssion profile of porcine embryonic and somatic cells

ABSTRACT: Relative MicroRNA expresssion profile of porcine embryonic and somatic cells

PROVIDER: PRJNA641018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12066447.fastq.gz	Fastqsanger.gz
	SRR12066448.fastq.gz	Fastqsanger.gz
	SRR12066449.fastq.gz	Fastqsanger.gz
	SRR12066450.fastq.gz	Fastqsanger.gz
	SRR12066451.fastq.gz	Fastqsanger.gz

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Relative MicroRNA expresssion profile of porcine embryonic and somatic cells

Project description:MicroRNAs (miRNAs) have been revealed to control the amount of mRNAs. miRNAs were known to be involved in the derivation and maintenance of pluripotent cells. However, the miRNA profile of pig pluripotent cells has not been defined well. Here, we report expression profiles of pluripotent and somatic (or differentiated) cells in pig to discover cell type-specific miRNAs for pluripotent and differentiated cells. Two blastocysts (BL) samples and embryonic stem cell-like (ES-like) cells were used for pluripotent cells. We selected embryoid bodies (EB) and fetal fibroblasts (PFF) as somatic cells. miRNAs were extracted from samples, then libraries were prepared to analyze miRNAs. We classified miRNAs into two categories, known and novel miRNAs. 72, 28, 19, 39 known miRNAs were relatively high in BL, ES-like, EB, and PFF, respectively. Also, expression levels of 15 and 22 known miRNAs were relatively high in pluripotent and differentiated cells. miRNAs that are well-known to control pluripotency did not found in our data. However, the list of cell type-specific miRNAs can be utilized to induce or maintain pluripotency in further studies. Therefore, our work will promote the application of miRNAs on pluripotency study in the pig.

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Project description:To investigate the effect of BRG1 overexpression in donor cells on the efficiency of porcine somatic cell nuclear transplantation. In total, 2358 differentially expressed genes were identified by the RNA-seq, with 1336 up- and 1022 down-regulated genes in the experimental group. The up-regulated genes were mainly enriched in PI3K/AKT signaling pathway and WNT signaling pathway, and the down-regulated genes were mainly enriched in disease development.

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The porcine microRNA transcriptome response to porcine cytomegalovirus infection

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BRG1 facilitates the development of porcine somatic cell nuclear transfer embryos

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Deciphering the porcine intestinal microRNA transcriptome

Project description:Background While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.

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