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Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
《农业科学与工程前沿（英文）》 2014年 第1卷 第1期 页码 77-84 doi: 10.15302/J-FASE-2014010
关键词： Larix transcriptome age wood formation somatic embryogenesis molecular marker
null
《医学前沿（英文）》 2015年 第9卷 第3期 页码 322-330 doi: 10.1007/s11684-015-0408-9
This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.
《农业科学与工程前沿（英文）》 2021年 第8卷 第2期
Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.
Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI
《农业科学与工程前沿（英文）》 2018年 第5卷 第2期 页码 214-225 doi: 10.15302/J-FASE-2018219
关键词： anthocyanin gene expression mutant purple-fleshed sweet potato transcriptome
null
《医学前沿（英文）》 2016年 第10卷 第1期 页码 61-75 doi: 10.1007/s11684-016-0436-0
The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.
关键词： Epstein-Barr virus paired-end transcriptome sequencing latency genes lytic genes nasopharyngeal carcinoma
Transcriptome analysis of wheat grain using RNA-Seq
Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI
《农业科学与工程前沿（英文）》 2014年 第1卷 第3期 页码 214-222 doi: 10.15302/J-FASE-2014024
关键词： transcriptome analysis wheat grain differentially expressed genes enrichment analysis
Exploring the cancer genome in the era of next-generation sequencing
null
《医学前沿（英文）》 2012年 第6卷 第1期 页码 48-55 doi: 10.1007/s11684-012-0182-x
The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.
关键词： next-generation sequencing cancer genome whole genome sequencing exome transcriptome
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《医学前沿（英文）》 2016年 第10卷 第3期 页码 297-310 doi: 10.1007/s11684-016-0452-0
Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.
关键词： erythroid differentiation hematopoietic stem cell RNA-seq miRNA lncRNA
Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN
《农业科学与工程前沿（英文）》 页码 215-230 doi: 10.15302/J-FASE-2021382
关键词： harvest season metabolites tea shoots transcriptomics untargeted metabolomics
大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征 Article
杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松
《工程（英文）》 2021年 第7卷 第11期 页码 1592-1602 doi: 10.1016/j.eng.2021.10.001
目前对胎盘哺乳动物脊髓发育的分子网络特征我们知之甚少。这些特征对深入理解与再生相关的重要生物过程和组织工程研究非常必要。现在，借助于从胚胎期到成年期大鼠脊髓的大规模时序转录组分析取得了一些新的进展。研究发现发育早期波动的RNA表达水平反映了脊髓活跃的转录调控并可能启动了脊髓的早期模式发育。脊髓发育过程中由microRNA (miRNA)和转录因子（TF）构成的宏观调控网络在新生期前后存在切换现象（即“镶嵌模型”）。差异可变剪接事件提示了可变剪接可能是郎飞结发育的驱动力之一。我们的研究也支持了脊髓中先天免疫的发育与其内在生长能力之间存在负相关性。发育过程中的一些表观遗传学修饰很可能在不同发育阶段发挥各自的调控功能。G蛋白偶联受体（包括嗅觉受体）可能在发育的轴突生长中发挥多效性作用。该研究为脊髓发育领域提供了有价值的资源，并与越来越多的单细胞数据形成互补，也为开发新的脊髓损伤组织工程策略提供了组学基础。
陈松林,徐文腾,陈张帆
《中国工程科学》 2019年 第21卷 第6期 页码 39-47 doi: 10.15302/J-SSCAE-2019.06.007
本文主要从基因组和转录组层面分析了极地动物基因资源的研究现状，梳理了本领域研究中存在的问题，并提出了未来发展战略。极地动物基因组测序起步较晚，迄今只完成了 13种极地动物的全基因组测序。在转录组研究方面，人们对极地的 31个物种进行了转录组测序，并在以下四个方向重点开展了研究：环境适应性研究；污染物应激反应的分子机制研究；不同发育阶段或不同组织中的转录组分析；功能基因挖掘。本领域研究由于起步晚，研究广度和深度都有待加强，但极地动物的基因资源研究具有战略意义。建议国家设立“极地动物基因资源发掘与应用”重点研发计划专项，围绕极地渔业动物特殊性状遗传解析、特有基因功能分析和基因工程产品研发等开展研究。
关键词： 极地动物 基因组，转录组，基因资源
Haiyan WANG, Qiaoxia ZHANG, Lilin YIN, Xiangdong LIU, Shuhong ZHAO, Mengjin ZHU, Changchun LI
《农业科学与工程前沿（英文）》 2017年 第4卷 第3期 页码 342-352 doi: 10.15302/J-FASE-2017162
单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article
张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟
《工程（英文）》 2022年 第17卷 第10期 页码 161-169 doi: 10.1016/j.eng.2021.05.009
了解重症新型冠状病毒肺炎（COVID-19）患者单核细胞的免疫学特征（包括与纤维化相关的特征）对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者（包括3名重症/危重症患者和4名普通型患者）和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本，包括重症/危重症时期血样3例，轻症时期血样4例，康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期，单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加，多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群：Mono 0和Mono 5。这两个亚群表达amphiregulin（AREG）、epiregulin（EREG）和细胞因子基因IL-18，KEGG分析显示富集的ErbB信号通路，这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变，包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群，可作为重症COVID-19的潜在预测因子和治疗靶点。
标题 作者 时间 类型 操作
Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
期刊论文
TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways
null
期刊论文
METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN
期刊论文
Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular
Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI
期刊论文
Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome
null
期刊论文
Transcriptome analysis of wheat grain using RNA-Seq
Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI
期刊论文
Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during
null
期刊论文
METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN
Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN
期刊论文
大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征
杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松
期刊论文
Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood
Haiyan WANG, Qiaoxia ZHANG, Lilin YIN, Xiangdong LIU, Shuhong ZHAO, Mengjin ZHU, Changchun LI
期刊论文
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