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Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 1,   Pages 77-84 doi: 10.15302/J-FASE-2014010

Abstract: In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in

Keywords： Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

Daniel Wai-Hung Ho,Alan Ka-Lun Kai,Irene Oi-Lin Ng

Frontiers of Medicine 2015, Volume 9, Issue 3,   Pages 322-330 doi: 10.1007/s11684-015-0408-9

Abstract:

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular

Keywords： TCGA     whole-transcriptome sequencing     HCC     liver cancer    

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clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

Frontiers of Medicine doi: 10.1007/s11684-023-1029-3

Abstract: clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

Keywords： tumor prognosis molecular     Microbiome subsets determine     center analysis microbiome     transcriptome data    

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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome
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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

Frontiers of Agricultural Science and Engineering 2018, Volume 5, Issue 2,   Pages 214-225 doi: 10.15302/J-FASE-2018219

Abstract: Sweet potato, , is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

Keywords： anthocyanin     gene expression     mutant     purple-fleshed sweet potato     transcriptome    

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Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Frontiers of Medicine 2016, Volume 10, Issue 1,   Pages 61-75 doi: 10.1007/s11684-016-0436-0

Abstract: However, comprehensive information through EBV transcriptome analysis in NPC is limited.

Keywords： Epstein-Barr virus     paired-end transcriptome sequencing     latency genes     lytic genes     nasopharyngeal carcinoma    

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Exploring the cancer genome in the era of next-generation sequencing

Hui Dong, Shengyue Wang

Frontiers of Medicine 2012, Volume 6, Issue 1,   Pages 48-55 doi: 10.1007/s11684-012-0182-x

Abstract: Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome

Keywords： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Frontiers of Medicine 2016, Volume 10, Issue 3,   Pages 297-310 doi: 10.1007/s11684-016-0452-0

Abstract: explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptomelevel, we took advantage of high throughput sequencing technologies to obtain transcriptome data from

Keywords： erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

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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

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 3,   Pages 214-222 doi: 10.15302/J-FASE-2014024

Abstract: Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation

Keywords： transcriptome analysis     wheat grain     differentially expressed genes     enrichment analysis    

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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

Frontiers of Agricultural Science and Engineering   Pages 215-230 doi: 10.15302/J-FASE-2021382

Abstract: We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome

Keywords： harvest season     metabolites     tea shoots     transcriptomics     untargeted metabolomics    

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Developmental Temporal Patterns and Molecular Network Features in the Transcriptome of Rat Spinal Cord Article

Jian Yang, Lili Zhao, Sheng Yi, Fei Ding, Yumin Yang, Yan Liu, Yongjun Wang, Mei Liu, Chengbin Xue, Lian Xu, Leilei Gong, Xinghui Wang, Yu Zhang, Bin Yu, Guo-li Ming, Xiaosong Gu

Engineering 2021, Volume 7, Issue 11,   Pages 1592-1602 doi: 10.1016/j.eng.2021.10.001

Abstract:

The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals, especially in terms of their relationships with vital biological processes such as regeneration. Here, using a large-scale temporal transcriptomic analysis of rat spinal cord from the embryonic stage to adulthood, we show that fluctuating RNA expression levels reflect highly active transcriptional regulation, which may initiate spinal cord patterning. We also demonstrate that microRNAs (miRNAs) and transcriptional factors exhibit a mosaic profile based on their expression patterns, while differential alternative splicing events reveal that alternative splicing may be a driving force for the development of the node of Ranvier. Our study also supports the existence of a negative correlation between innate immunity and intrinsic growth capacity. Epigenetic modifications appear to perform their respective regulatory functions at different stages of development, while guanine nucleotide-binding protein (G protein)-coupled receptors (including olfactory receptors (ORs)) may perform pleiotropic roles in axonal growth. This study provides a valuable resource for investigating spinal cord development and complements the increasing number of single-cell datasets. These findings also provide a genetic basis for the development of novel tissue engineering strategies.

Keywords： Development     Gene expression pattern     Innate immunity     Spinal cord     Transcriptome    

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Polar Animal Genetic Resources: Current Situation and Development Strategies

Chen Songlin, Xu Wenteng, Chen Zhangfan

Strategic Study of CAE 2019, Volume 21, Issue 6,   Pages 39-47 doi: 10.15302/J-SSCAE-2019.06.007

Abstract: Transcriptome sequencing has been carried out for 31 polar animals in recent years, and the transcriptomefocused on adaption to polar environments, molecular mechanisms in response to pollutant stresses, transcriptome

Keywords： polar animal     genome     transcriptome     genetic resources    

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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

Frontiers of Agricultural Science and Engineering 2017, Volume 4, Issue 3,   Pages 342-352 doi: 10.15302/J-FASE-2017162

Abstract: Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes (DEGs) in extreme response (ER) pigs and 192 DEGs in moderate response (MR) pigs. Most DEGs were related to immune responses, included , , , , , , , and . Gene ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation, immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals.

Keywords： neutrophil     peripheral blood     pig     poly I:C     transcriptome    

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Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-Cell Transcriptome Article

Yan Zhang, Shuting Wang, He Xia, Jing Guo, Kangxin He, Chenjie Huang, Rui Luo, Yanfei Chen, Kaijin Xu, Hainv Gao, Jifang Sheng, Lanjuan Li

Engineering 2022, Volume 17, Issue 10,   Pages 161-169 doi: 10.1016/j.eng.2021.05.009

Abstract:

Understanding the immunological characteristics of monocytes—including the characteristics associated with fibrosis—in severe coronavirus disease 2019 (COVID-19) is crucial for understanding the pathogenic mechanism of the disease and preventing disease severity. In this study, we performed single-cell transcriptomic sequencing of peripheral blood samples collected from six healthy controls and 14 COVID-19 samples including severe, moderate, and convalescent samples from three severely/critically ill and four moderately ill patients. We found that the monocytes were strongly remodeled in the severely/critically ill patients with COVID-19, with an increased proportion of monocytes and seriously reduced diversity. In addition, we discovered two novel severe-disease-specific monocyte subsets: Mono 0 and Mono 5. These subsets expressed amphiregulin (AREG), epiregulin (EREG), and cytokine interleukin-18 (IL-18) gene, exhibited an enriched erythroblastic leukemia viral oncogene homolog (ErbB) signaling pathway, and appeared to exhibit pro-fibrogenic and pro-inflammation characteristics. We also found metabolic changes in Mono 0 and Mono 5, including increased glycolysis/gluconeogenesis and an increased hypoxia inducible factor-1 (HIF-1) signaling pathway. Notably, one pre-severe sample displayed a monocyte atlas similar to that of the severe/critical samples. In conclusion, our study discovered two novel severe-disease-specific monocyte subsets as potential predictors and therapeutic targets for severe COVID-19. Overall, this study provides potential predictors for severe disease and therapeutic targets for COVID-19 and thus provides a resource for further studies on COVID-19.

Keywords： COVID-19     Severe infection     Critically ill     Monocytes     Fibrosis    

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Intratumoral Bacteria Dysbiosis Is Associated with Human Papillary Thyroid Cancer and Correlated with Oncogenic Signaling Pathways Article

Shuang Yu, Yanqiang Ding, Xuejie Wang, Siu Kin Ng, Siting Cao, Weixin Liu, Zhuming Guo, Yubin Xie, Shubin Hong, Lixia Xu, Xiaoxing Li, Jie Li, Weiming Lv, Sui Peng, Yanbing Li, Joseph J.Y. Sung, Jun Yu, Haipeng Xiao

Engineering 2023, Volume 28, Issue 9,   Pages 179-192 doi: 10.1016/j.eng.2023.01.007

Abstract: In parallel, we performed microbial profiling and transcriptome
sequencing in the tumor and adjacent

Keywords： Papillary thyroid cancer     Benign thyroid nodule     Bacteria     Transcriptome     Hashimoto's thyroiditis    

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Title Author Date Type Operation

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

Journal Article

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

Daniel Wai-Hung Ho,Alan Ka-Lun Kai,Irene Oi-Lin Ng

Journal Article

clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

Journal Article

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

Journal Article

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

Journal Article

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Journal Article

Exploring the cancer genome in the era of next-generation sequencing

Hui Dong, Shengyue Wang

Journal Article

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Journal Article

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

Journal Article

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

Journal Article

Developmental Temporal Patterns and Molecular Network Features in the Transcriptome of Rat Spinal Cord

Jian Yang, Lili Zhao, Sheng Yi, Fei Ding, Yumin Yang, Yan Liu, Yongjun Wang, Mei Liu, Chengbin Xue, Lian Xu, Leilei Gong, Xinghui Wang, Yu Zhang, Bin Yu, Guo-li Ming, Xiaosong Gu

Journal Article

Polar Animal Genetic Resources: Current Situation and Development Strategies

Chen Songlin, Xu Wenteng, Chen Zhangfan

Journal Article

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

Journal Article

Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-Cell Transcriptome

Yan Zhang, Shuting Wang, He Xia, Jing Guo, Kangxin He, Chenjie Huang, Rui Luo, Yanfei Chen, Kaijin Xu, Hainv Gao, Jifang Sheng, Lanjuan Li

Journal Article

Intratumoral Bacteria Dysbiosis Is Associated with Human Papillary Thyroid Cancer and Correlated with Oncogenic Signaling Pathways

Shuang Yu, Yanqiang Ding, Xuejie Wang, Siu Kin Ng, Siting Cao, Weixin Liu, Zhuming Guo, Yubin Xie, Shubin Hong, Lixia Xu, Xiaoxing Li, Jie Li, Weiming Lv, Sui Peng, Yanbing Li, Joseph J.Y. Sung, Jun Yu, Haipeng Xiao

Journal Article