title: Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken.
abstract: Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Kunpeng
authors.initials: K
authors.lastname: Han
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Genxi
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Jinyu
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Kaizhou
authors.initials: K
authors.lastname: Xie
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.|Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Xue
authors.affiliation: Vazyme Biotech Co.,Ltd., Economic and Technological Development Zone, Nanjing, Jiangsu, China.
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Fan
mesh_terms: D017667:Adipocytes / Q000166:cytology / Q000378:metabolism; D000818:Animals; D002454:Cell Differentiation; D002478:Cells, Cultured; D002645:Chickens / Q000235:genetics; D016000:Cluster Analysis; D015870:Gene Expression; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger