Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep
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PROVIDER: PRJNA450541 | ENA |
REPOSITORIES: ENA
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Project description:We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the Qianhua Mutton Merino (QHMM) and Small Tail Han (STH) sheep.We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH.The genome-wide transcriptome analysis of QHMM and STH muscle in present study is reported first time.
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Project description:In this study, we selected differentially expressed miRNAs through construcing and analyzing the miRNA expression profile during 2-, 6-, and 12- month-old Small Tail Han Sheep ovaries, which provided a theoretical basis for the study of miRNAs regulating the reproduction of Small Tail Han Sheep. RNASeq techniques were used to perform profile analysis for these ovaries. The results showed that 11, 13 and 19 DE miRNAs were identified in 2- vs 6-, 6- vs 12-, and 2- vs 12-month-old ovaries, respectively. In total, 54, 37, and 198 predicted target genes of DE miRNAs were obtained from these three groups, respectively. GO and KEGG analyses showed that, in 2- vs 6-month-olds, the target genes of DE known sheep miRNAs were involved in 102 GO terms and 7 signaling pathways; in 6- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 52 GO terms and 3 signaling pathways; and in 2- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 88 GO terms and 6 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. 9 miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-432 with RPS6KA1 was validated by a dual luciferase reporter gene detection system. This is the first integrative analysis of miRNA and mRNA expression profiles in Small Tail Han Sheep ovarian development. These data help elucidate the molecular regulatory mechanisms in sheep ovarian development and identify the biomarkers that influence reproductive performance of Small Tail Han Sheep ewe.
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Project description:We aimed to evaluated the key microRNA-mRNA network associated with sheep muscle growth and development. We used RNA-Seq to obtain the smallRNA profiles of the longissimus muscle from the QHMM and STH. The results showed that a total of 153 known sheep miRNAs were identified, and 4 known sheep miRNAs were differently expressed. Combining mRNA library data, 26 target genes of 4 known miRNAs were selected and the miRNA–mRNA network was successfully built. GO and KEGG analysis showed that 26 target genes were significantly enriched in 86 biological processes, including muscle organogenesis, myoblast migration, cell proliferation, and adipose tissue development, and nine metabolic pathways, including carbohydrate, nucleotide, and amino acid metabolic pathways. The oar-miR-655-3p and target gene ACSM3, and oar-miR-381-5p and target gene ABAT were selected for subsequent analysis based on GO and KEGG analyses. The results suggested that the DEmiRNAs, especially oar-miR-655-3p and oar-miR-381-5p play crucial roles in muscle growth and development processes. This Integrative analysis of microRNA-mRNA analysis of QHMM and STH muscle is reported for the first time.
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Project description:Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep
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Project description:Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep All pair comparison of 5 pigmentation samples with dye swaps. Dye swaps were performed with different biological replicates (labelled 1 or 2) NOR - White sample from a normal, non-affected wild-type individual sheep PBB - Black sample from a piebald individual sheep PBW - White sample from a piebald individual sheep RSB - Black sample from a recessive black sheep RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area.
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Project description:We performed a genome-wide analysis of mRNAs and lncRNAs from Small Tail Han sheep of genotypes FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) and from Dorset sheep (Dorset) to identify potential regulators of fecundity. An integrated analysis revealed significantly correlated patterns of expression. Dramatic changes of mRNAs and lncRNAs suggest their critical roles in sheep fecundity. This study provides a novel view of the regulatory mechanisms involved in sheep fecundity.
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Project description:We report the application of High throughout sequencing to explore the differences of skin between Super Merino sheep(SM) and Small Tail Han sheep, which have remarkable phenotype differences on wool and hair follicle traits. We analysed the expression data by CLC genomic workbench 9.0 software. We find there are 435 differential expressional genes (DEGs) (127 were up-regulated and 308 were down-regulated) when STH sheep as control group. Some hair follicle KRTs, KAPs genes and hair follicle stem cells marker genes, were up-regulated in SM sheep. However, some of mammalian epidermal development complex (EDC) family genes were up-regulated in STH sheep. The GO and gene network analysis shown high expression genes in SM sheep enriched on type I interferon, lipid/fatty acid synthesis metabolism. This study provide more details in skin which control the development of follicle and wool in sheep.
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Project description:The semen of Small Tail Han Sheep has characteristics of high yield, high density, and good motility. To reveal the key miRNAs, mRNAs and miR-Targets regulatory mechanisms in Small Tail Han Sheep testes development, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes were investigated by RNA-seq technology and bioinformatics methods. As the results shown: 630, 102, and 322 differentially expressed (DE) mRNAs; 5, 1 and 4 DE known miRNAs; 132, 105 and 24 DE novel miRNAs were identified in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes, respectively. GO and pathway analysis showed: in 2- vs 6-month-old testes, DE mRNAs were mainly involved in sexual maturation process and the DE mRNAs were mainly involved in multiple metabolism and biosynthesis pathways; in 6- vs 12-month-old testes, DE mRNAs were mainly involved in metabolism and translation processes, and the most significant pathway that DE mRNAs involved in was ribosome pathway; in 2- vs 12-month-old testes, DE mRNAs were mainly involved in metabolism and physiological processes, and DE mRNAs were mainly involved in multiple metabolism and biosynthesis pathways. Subsequently, 76, 11 and 1 DE miR-Targets were identified in 2- vs 6-month-old, 2- vs 12-month-old, and 6- vs 12-month-old testes, respectively. 3 miR-Target regulatory networks were constructed based on these miR-Targets, which helped to elucidate the regulatory metabolism in Small Tail sheep testes development. Finally, 6 miRNAs and 7 mRNAs were selected to validate the RNA-seq data by RT-PCR.
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Project description:Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep
| PRJNA335752 | ENA
Project description:Purpose: To investigaet whether an inflammatory immune response at the Ileum can contribute to development and severity of diarrhoea in Merino sheep that are prone and not prone to develop diarrhoea. Methods:Transcriptomes in the Ileum (third part of small intestine) of Merino sheep were analyzed using RNASeq. Functional enrichment of DEGs using GO terms in biological processes and KEGG pathways were studied. PPI (protein-protein interaction) network and sub-network were studied using clusterONE plugin in Cytoscape. Result and conclusion: Although Ileum in not a primary site of helminth (species under study in our experiment), the results indicated that an inflammatory immune response can contribute to development and severity of diarrhoea. The low-diarrhoea animals did not show any signs of immune/inflammatory response. The genes with important roles in the responses to helminth infection could be targeted in breeding programs to prevent diarrhoea.
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