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Wei Chen,Guo‑feng Fang,Shou‑dong Wang,Hui Wang,Yong‑qing Zeng 한국유전학회 2017 Genes & Genomics Vol.39 No.7
The pig provides meat products for human consumption on a large scale. High-throughput sequencing technology provides a powerful approach for the characterization of the muscle transcriptome of pigs. Despite many studies using high-throughput technologies, the functional complexity of porcine muscle transcriptome is not fully elucidated. Therefore, the aim of this study was to gain insight into the longissimus lumborum muscle transcriptome between two pig breeds with distinct phenotypes, Laiwu pig, a Chinese indigenous pig breed, and Yorkshire pig, a Western breed. RNA-seq was applied to sample transcripts of the longissimus lumborum muscle between the two pig breeds to gain insights into wholegenome transcription profiles. For the Laiwu and Yorkshire libraries, we obtained a total of 40,498,476 and 59,072,892 high quality reads, respectively. Moreover, the resulting data set provided expression patterns for many annotated, predicted and novel pig genes. 178 significantly differentially expressed genes were identified between the Laiwu and Yorkshire pigs, with 98 up-regulated and 80 downregulated genes in Laiwu pig compared with Yorkshire pig. Gene expression results of the RNA-seq data were validated by qRT-PCR for twelve genes. Genes that were differentially expressed were involved in lipid metabolism and were more highly expressed in Laiwu pigs. The present study provides a comprehensive view of differences in the muscle transcriptome between two pig phenotypes. These results expand our knowledge of the genes transcribed in the skeletal muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the phenotypic differences on meat quality.
Wei Chen,Guo-Feng Fang,Shou-Dong Wang,Hui Wang,Yong-Qing Zeng 한국유전학회 2017 Genes & Genomics Vol.39 No.2
The domestic pig is an important agricultural animal used as a source of meat worldwide. As an important resource, Laiwu pig has some special characteristics compared with Yorkshire pig. It is necessary to identify the differentially expressed microRNAs (miRNAs) in skeletal muscle between two pig breeds. Therefore, we herein performed a comprehensive investigation for miRNA transcriptome of skeletal muscle from the two pig breeds. On average, we obtained approximately 13,493,607 clean reads in Laiwu pig and 12,938,257 clean reads in Yorkshire pig in this study. Totally, 265 known miRNAs were identified, and among these, 229 miRNAs were expressed in all the six pigs. From the 265 known miRNAs, 19 of these miRNAs were found significantly differentially expressed (q\0.05). Of these significantly expressed miRNAs, seven miRNAs were significantly upregulated and 12 miRNAs were down-regulated in Laiwu pig compared with Yorkshire pig. Among the significantly expressed miRNAs, ssc-miR-194-5p has the largest foldchange (6.35-fold). Ten differentially expressed miRNAs selected from high throughput sequencing were confirmed by real-time RT-PCR (RT-qPCR), and the results indicated that the expression patterns were consistent with sequencing results. Our results not only present a comprehensive miRNA transcriptome profile of skeletal muscle between two pig breeds with distinct phenotypes, but also could be useful for investigating the functions of differentially expressed miRNAs associated with the phenotype traits.
Exploration of Molecular Mechanisms of Diffuse Large B-cell Lymphoma Development Using a Microarray
Zhang, Zong-Xin,Shen, Cui-Fen,Zou, Wei-Hua,Shou, Li-Hong,Zhang, Hui-Ying,Jin, Wen-Jun Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.3
Objective: We aimed to identify key genes, pathways and function modules in the development of diffuse large B-cell lymphoma (DLBCL) with microarray data and interaction network analysis. Methods: Microarray data sets for 7 DLBCL samples and 7 normal controls was downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified with Student's t-test. KEGG functional enrichment analysis was performed to uncover their biological functions. Three global networks were established for immune system, signaling molecules and interactions and cancer genes. The DEGs were compared with the networks to observe their distributions and determine important key genes, pathways and modules. Results: A total of 945 DEGs were obtained, 272 up-regulated and 673 down-regulated. KEGG analysis revealed that two groups of pathways were significantly enriched: immune function and signaling molecules and interactions. Following interaction network analysis further confirmed the association of DEGs in immune system, signaling molecules and interactions and cancer genes. Conclusions: Our study could systemically characterize gene expression changes in DLBCL with microarray technology. A range of key genes, pathways and function modules were revealed. Utility in diagnosis and treatment may be expected with further focused research.