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Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig

ABSTRACT: Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig

PROVIDER: PRJNA516660 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8478240_1.fastq.gz	Fastqsanger.gz
	SRR8478240_2.fastq.gz	Fastqsanger.gz
	SRR8478241_1.fastq.gz	Fastqsanger.gz
	SRR8478241_2.fastq.gz	Fastqsanger.gz
	SRR8478242_1.fastq.gz	Fastqsanger.gz

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Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig

Project description:Skin is the largest organ of body, and one function of skin is protecting underly organs away from ultraviolet (UV) radiation damage. Loss of melanocyte will reduce ability of skin to against UV radiation damage. We found Bama Pig can be an ideal model studying loss of melanocyte. In this study, we performed transcriptome profiling of mRNA and long noncoding RNA in Bama pig white skin (absence of melanocyte) and black skin (existence of melanocyte) to provide dataset for clinical researches. Total of 14,900 mRNAs and 7,566 lncRNAs were expressed in the study. Results of hierarchical cluster analysis and principal component analysis (PCA) demonstrated expression of mRNAs and lncRNAs varied greatly between two color skins. 2,342 mRNA were identified as being differentially expressed, including 1,309 genes that were down-regulated in white skin and 1,033 gene that were up-regulated in white skin (P <0.05; |log2(fold change)| > 1). The genes down-regulated in white skin were associated with melanocyte biology, melanocyte function and keratin, while genes up-regulated in white skin were main associated with metabolism pathway, oxidative phosphorylation and citrate cycle (TCA cycle). In addition, we identified 120 differentially expressed lncRNAs. In those lncRNAs, 4 lncRNAs may function in skin biology (TCONS_00019024 and TCONS_00077733) or metabolic (TCONS_00042201 and TCONS_00060772). Our research provides Bama pig skins datasets and could promote clinical researches utilizing Bama pig as model.

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The ChIP_seq of pituitary gland from Bama Xiang and Large White pigs

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Distinct Patterns of Insulin response, sexual development, organ size regulation in postnatal developing Subcutaneous and Visceral fat of Bama Pig

Project description:In this study, the SAF and VAF development was characterized and compared in SAF and VAF of Bama pig during postnatal development (infancy, puberty and adulthood) using RNA sequencing technologies (RNA-Seq). We profiled the transcriptome of SAF and VAF isolated from 1-, 3- and 6-month-old pigs and identified 23636 expressed transcription units. Of the them, 1165 genes were differentially expressed between the despots and /or developmental stages. Upregulated gene in SAF of Bama pigs showed significant function and pathway enrichment in central nervous system development, lipid metabolism, oxidation-reduction process, cell adhesion while genes involved in immune system process, actin cytoskeleton organization, male gonad development, hippo signaling pathway preferentially expressed in VAF. Short time-series expression miner analysis demonstrated the differentiation in gene expression patterns between the two deposit was corresponding to their distinct responses in sextual development, hormone signaling pathway, lipid metabolism as well as hippo signaling pathway. Transcriptome analysis of SAF and VAF in Bama pigs suggested that the depot differences of the adipose tissue are not only related to lipid metabolism and endocrine function, but also closely associated with sextual development and organ size regulation.

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Project description:The use of single-cell sequencing technology for single-cell transcriptomics studies in pigs is expanding progressively. However, the comprehensive classification of cell types across different anatomical tissues and organs of pigs in multiple datasets remains relatively limited. This study centers on an investigation using single-cell sequencing technology in Bama pigs, where unique marker genes and their corresponding transcriptomic profiles have been identified for diverse cell types across distinct anatomical tissues and organs, encompassing subcutaneous fat, visceral fat, skeletal muscle, liver, spleen, lung, and kidney. Using comprehensive data analyses, we discovered the widespread cellular diversity inherent in different anatomical tissues and organs of Bama pigs. This study not only provides a pivotal dataset for physiological research on Bama pigs but also contributes to the verification and prediction of key marker genes in the single-cell transcriptomics of these tissues and organs. Furthermore, the data and methodologies that were used in this study underscore our commitment to enhancing the authenticity of cell type identification and ensuring the consistency in cell type allocation.

2023-12-22 | GSE241555 | GEO

The antimicrobial peptide Magainin-2 interacts with BamA impairing folding of E. coli membrane proteins

Project description:In this paper we investigated the mechanism of action of Maganin-2 (Mag-2), a well-known antimicrobial peptide isolated from the African clawed frog Xenopus laevis, by functional proteomic approaches. Several proteins belonging to E. coli macromolecular membrane complexes were identified as Mag-2 putative interactors. Among these, we focused our attention on BamA a membrane protein belonging to the BAM complex responsible for the folding and insertion of nascent β‐barrel Outer Membrane Proteins (OMPs) in the outer membrane. In silico predictions by molecular modelling and in vitro fluorescence binding and Light Scattering experiments carried out using a recombinant form of BamA confirmed the formation of a stable Mag-2/BamA complex and indicated a high affinity of the peptide for BamA. The functional implications of these interactions were investigated by two alternative and complementary approaches. The number of outer membrane proteins OmpA and OmpF produced in E. coli following Mag-2 incubation was evaluated by both western blot analysis and quantitative tandem mass spectrometry in MRM scan mode. In both experiments, a gradual decrease in outer membrane protein production with time was observed because of Mag-2 treatment.

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