05月03 【成功案例】百邁客云 真核生物有參考基因組的轉(zhuǎn)錄組分析平臺(tái) 助力 王金玉老師 發(fā)表《雞中腹部前脂肪細(xì)胞分化過(guò)程中l(wèi)ncRNA和mRNA表達(dá)的全基因組分析》
摘要：
長(zhǎng)非編碼RNA（lncRNA）調(diào)節(jié)脂肪形成和其他與代謝組織發(fā)育和功能相關(guān)的過(guò)程。然而，關(guān)于雞中前脂肪細(xì)胞分化期間lncRNAs的功能和特征卻知道的很少，本文使用RNA測(cè)序分析不同分化階段的前脂肪細(xì)胞中的lncRNA和mRNA表達(dá)。從12個(gè)樣本總共獲得了1,300,074,528 clean reads和27,023個(gè)新的LncRNA，在各個(gè)階段差異表達(dá)的基因（1,336個(gè)lncRNA和1,759個(gè)mRNA；總共3,095個(gè)）的數(shù)量隨著細(xì)胞分化而下降。這些差異基因參與前脂肪細(xì)胞分化的幾個(gè)廣泛研究的途徑，包括甘油脂代謝，哺乳動(dòng)物中雷帕霉素的靶標(biāo)，過(guò)氧化物酶體增殖物激活受體和絲裂原活化蛋白激酶信號(hào)通路，而在本研究中，首次報(bào)道了一些與前脂肪細(xì)胞分化相關(guān)的通路，包括丙酸代謝，脂肪酸代謝和氧化磷酸化途徑。此外，通過(guò)k-means均值聚類，3,095個(gè)差異基因被聚成8個(gè)表達(dá)模式。其中，K2這一簇基因中在前脂肪細(xì)胞分化中起著重要作用，使用加權(quán)共表達(dá)網(wǎng)絡(luò)分析（WGCNA），鑒定了與A0（第0天），A2（第2天）和A6（第6天）階段相關(guān)的6個(gè)階段特異性模塊，隨后從階段特異性模塊鑒定了9個(gè)中心，高度相關(guān)的基因，包括：XLOC_068731, XLOC_022661, XLOC_045161, LOC_070302, CHD6, LLGL1, NEURL1B, KLHL38,?和ACTR6。本研究為進(jìn)一步研究雞的lncRNA提供了寶貴的資源，有利于更好的了解雞的前脂肪細(xì)胞分化。
本文主要用了云平臺(tái)中的WGCNA和k-means均值聚類。
英文摘要：
Long noncoding RNAs (lncRNAs) regulate adipogenesis and other processes associated with metabolic tissue development and function. However, little is known about the function and profile of lncRNAs during preadipocyte differentiation in the chicken (Gallus gallus). Herein, lncRNA and mRNA expression in preadipocytes at different stages of differentiation were analyzed using RNA sequencing. A total of 1,300,074,528 clean reads and 27,023 novel lncRNAs were obtained from 12 samples. The number of genes (1336 lncRNAs and 1759 mRNAs; 3095 in total) differentially expressed across various stages declined as differentiation progressed. Differentially expressed genes were found to be involved in several pathways related to preadipocyte differentiation that have been extensively studied, including glycerolipid metabolism, and the mammalian target of rapamycin, peroxisome proliferator-activated receptor, and mitogen-activated protein kinase signaling pathways. To our knowledge, some pathways are being report- ed for the first time, including the propanoate metabolism, fatty acid metabolism, and oxidative phosphor- ylation pathways. Furthermore, 3095 differentially expressed genes were clustered into eight clusters, and their expression patterns were determined through K-means clustering. Genes involved in the K2 cluster likely play important roles in preadipocyte differentiation. Six stage-specific modules related to A0 (day 0), A2 (day 2), and A6 (day 6) stages were identified, using weighted coexpression network analysis. Nine central, highly connected .genes in stage-specific modules were subsequently identified, including XLOC_068731, XLOC_022661, XLOC_045161, XLOC_070302, CHD6, LLGL1, NEURL1B, KLHL38, and ACTR6. This study provides a valuable resource for further study of chicken lncRNA and facilitates a better understanding of preadipocyte differentiation in the chicken.