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MP3RNA-seq:Massively parallel 3’end RNA sequencing for high-throughput gene expression profiling and genotyping

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Journal of Integrative Plant Biology 2021年第7期63卷 1227-1239页

作者： Jian Chen Xiangbo Zhang Fei Yi Xiang Gao Weibin Song Haiming Zhao Jinsheng Lai State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China

Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression ***,its application tolarge‐scale experiments remains limited by costand labor *** we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this ***3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and ***3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also *** its utility,we applied MP3RNA‐seqto 477 double haploid lines of *** iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for *** with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative *** conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.

关键词： gene expression profiling genotyping maize MP3RNA‐seq quantitative trait loci

Analysis of Pathway Activity in Primary Tumors and NCI60 Cell Lines Using gene expression profiling Data

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Genomics, Proteomics & Bioinformatics 2007年第1期5卷 15-24页

作者： Xing-Dong Feng Shu-Guang Huang Jian-Yong Shou Bi-Rong Liao Jonathan M. Yingling Xiang Ye Xi Lin Lawrence M. Gelbert Eric W. Su Jude E. Onyia Shu-Yu Li Integrative Biology Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Global Discovery ＆ Development Statistics Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Cancer Discovery Research Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA

To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in -70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-β, TNF-α, Src, Myc, E2F3, and β-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and/or Src, but not E2F3, β-catenin, TNF-α, or TGF-β pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The ＂gene expression pathway signatures＂ we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.

关键词： cancer pathways gene expression profiling supervised learning classification

Discovery of molecular associations among aging, stem cells, and cancer based on gene expression profiling

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Chinese Journal of Cancer 2013年第4期32卷 155-161页

作者： Xiaosheng Wang Biometric Research Branch National Cancer InstituteNational Institutes of Health

The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experimental approach. I reviewed several reports that used a bioinformatics approach to analyze the associations among aging, stem cells, and cancer by microarray gene expression profiling. The high expression of aging- or human embryonic stem cell-related molecules in cancer suggests that certain important mechanisms are commonly underlying aging, stem cells, and cancer. These mechanisms are involved in cell cycle regulation, metabolic process, DNA damage response, apoptosis, p53 signaling pathway, immune/inflammatory response, and other processes, suggesting that cancer is a developmental and evolutional disease that is strongly related to aging. Moreover, these mechanisms demonstrate that the initiation, proliferation, and metastasis of cancer are associated with the deregulation of stem cells. These findings provide insights into the biology of cancer. Certainly, the findings that are obtained by the informatics approach should be justified by experimental validation. This review also noted that next-generation sequencing data provide enriched sources for cancer informatics study.

关键词： Cancer aging stem cells gene expression profiling Cancer informatics

Molecular subtypes identified by gene expression profiling in early stage endometrioid endometrial adenocarcinoma

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Chinese Medical Journal 2013年第19期126卷 3680-3684页

作者： GAO Bao-rong CHEN Yong-hua YAO Yuan-yang LI Xiao-ping WANG jian-liu WEI Li-hui Department of Obstetrics and Gynecology Peking UniversityPeople's Hospital Beijing 100044 China

Background Early stage （FIGO stage Ⅰ-Ⅱ） endometrioid endometrial adenocarcinoma （EEA） is very common in clinical ***,patients with the early stage EEA show various clinical behaviors due to biological ***,we aimed to discover distinct classes of tumors based on gene expression profiling,and analyze whether the molecular classification correlated with the histopathological stages or other clinical *** Hierarchical clustering was performed for class discovery in 28 eady stage EEA samples using a special cDNA microarray chip containing 492 genes designed for endometrial *** between clinicopathologic parameters and our classification were *** the significance analysis of microarrays （SAM） array was used to identify the signature genes according to the tumor grade and myometrial *** Three tumor subtypes （subtypes Ⅰ,Ⅱ and Ⅲ） were identified by hierarchical clustering,each subtype had different clinicopathological factors,such as tumor grade,myometrial invasion status,and FIGO ***,SAM analysis showed 34 up-regulated genes in high grade tumors,and 38 up-regulated genes and 1 down-regulated in deep myometrial invasive *** overlap genes between these two high-risk factors were markedly up-regulated in subtype Ⅰ,but down-regulated in subtype Ⅲ.Conclusion We have identified novel molecular subtypes in early stage *** gene signatures characterize each tumor subtype,which could be used for recognizing the tumor risk and providing a basis for further treatment stratification.

关键词： endometrioid adenocarcinoma molecular classification gene expression profiling risk factor

MP3RNA-seq:massive parallel 3' end RNA-seq for highthroughput gene expression profiling

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MP3RNA-seq:massive parallel 3' end RNA-seq for highthroughpu...

Identification of risk factor for sepsis-related death by gene expression profiling analysis

2018中国作物学会学术年会

作者：陈建 Xiangbo Zhang Fei Yi Xiang Gao Weibin Song Haiming Zhao 赖锦盛 State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural University

Genome-wide gene expression profiling is fundamental for various biological researches *** generation sequencing based RNA-seq is now nearly the routine method of ***,the current RNA-seq approach is not suitable for high throughput experiments due to cost and labor *** we describe a massive parallel 3’ end RNA-seq(MP3 RNA-seq) method,which can generate the sequencing reads of the 3’end of mRNAs for hundreds or thousands of samples in one single *** sequence information resulted from MP3 RNA-seq is sufficient for gene expressional quantification and can also be used for *** further demonstrate its application,we generated the MP3 RNA-seq data for 477 double haploid lines of maize,which were then using for high resolution eQTL and agronomic trait QTL *** summary,MP3 RNA-seq is highly reproducible,accurate,and sensitive for high throughput gene expression profiling,and it can be generally applicable in most of the eukaryotic species.

关键词： MP3RNA-seq gene expression profiling genotyping QTL mapping

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Identification of risk factor for sepsis-related death by ge...

Comprehensive genomic analysis and expression profiling of cysteine-rich polycomb-like transcription factor gene family in tea tree

第十二届全国免疫学学术大会

作者： Qi Yan Chen Xinxin Wu Na Cui Xueling Liu Zhonghui Department of Immunology College of Basic Medical SciencesJilin University Department of genetics College of Basic Medical SciencesJilin University

Sepsis is the common cause of death from systemic *** many efforts have been devoted for this life-threatening condition,it remains a lack of risk factor to evaluate the severity of *** we focused on the identificatio... 详细信息

关键词： Sepsis gene expression profiling Survivor Risk factor IFN-I signaling

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Horticultural Plant Journal 2021年第5期7卷 469-478页

作者： Hong Nan Yanglei Lin Xinghua Wang Lizhi Gao Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of SciencesKunming 650201China University of the Chinese Academy of Sciences Beijing 100039China Yunnan Pu’er Tea Tree Breeding Station Pu Er 665099China Institution of Genomics and Bioinformatics South China Agricultural UniversityGuangzhou 510642China

Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress *** CPP transcription factors have been characterized in several other plant species,a genome-wide characterization of the CPP gene family has been absent in Camellia *** this study,we totally identified 7,8,and 8 non-redundant CsCPP genes in three published genomes,including Camellia sinensis *** ***-10(CSA-YK10),Camellia sinensis *** ***(CSS-BY)and Camellia sinensis *** ***(CSS-SCZ).CPP proteins from tea tree and other plant species were classified into three groups,which were further divided into four subgroups based on phylogenetic *** CPP genes in the same subgroup had similar gene structures and conserved *** cis-acting elements analysis indicated that CPP genes might be involved in plant growth,development and stress *** of gene expression using qRT-PCR experiments validated that CPP genes exhibited different expression patterns across the examined *** the genes were expressed differentially in a range of tissues,indicating that CPPs were involved in a range of developmental and physiological *** study has obtained new insights into the evolution and function of the CPP gene family in the growth and development of tea plants,and also provide candidate genes for further functional characterization in tea tree.

关键词： Camellia sinensis CPP transcription factor Genome-wide analysis gene expression profiling

Identification of biomarkers of human pancreatic adenocarcinomas by expression profiling and validation with gene expression analysis in endoscopic ultrasound-guided fine needle aspiration samples

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World Journal of Gastroenterology 2006年第21期12卷 3344-3351页

作者： Henrik Laurell Michèle Bouisson Philippe Berthelémy Philippe Rochaix Sébastien Déjean Philippe Besse Christiana Susini Lucien Pradayrol Nicole Vaysse Louis Buscail INSERM U531 IFR31 Institut Louis BugnardBP 8422531432 Toulouse Cedex 4France Service de Gastroentérologie Centre Hospitaller de Pau PauFrance Laboratoire d'Anatomo-Pathologie Institut Claudius Regaud ToulouseFrance Laboratoire de Statistique et Probabilités Université Paul Sabatier ToulouseFrance INSERM U531 IFR31 Institut Louis BugnardBP 8422531432 Toulouse Cedex 4France Service de Gastroenterologie et de la NutritionCHU RangueilToulouseFrance

AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differentially expressed genes and to validate the differential expression of a subset of genes by quantitative real-time RT-PCR （RT-QPCR） in endoscopic ultrasound-guided fine needle aspiration （EUS-guided FNA） ***： Commercially dedicated cancer cDNA macroarrays （Atlas Human Cancer 1.2） containing 1176 genes were used. Different statistical approaches （hierarchical clustering, principal component analysis （PCA） and SAM） were used to analyze the expression data. RT-QPCR and immunohistochemical studies were used for validation of ***： RT-QPCR validated the increased expression of LCN2 （lipocalin 2） and for the first time PLAT （tissue-type plasminogen activator or tPA） in malignant pancreas as compared with normal pancreas. Immunohistochemical analysis confirmed the increased expression of LCN2 protein localized in epithelial cells of ducts invaded by carcinoma. The analysis of PLAT and LCN2 transcripts in 12 samples obtained through EUS-guided FNA from patients with pancreatic adenocarcinoma showed significantly increased expression levels in comparison with those found in normal tissues, indicating that a sufficient amount of high quality RNA can be obtained with this ***： expression profiling is a useful method to identify biomarkers and potential target genes. Molecular analysis of EUS-guided FNA samples in pancreatic cancer appears as a valuable strategy for the diagnosis of pancreatic adenocarcinomas.

关键词： Pancreas Colon Adenocarcinoma gene expression profiling Endoscopic ultrasonography Ultrasound Fine needle aspiration

Transcription profiling using RNA-Seq demonstrates expression differences in the body walls of juvenile albino and normal sea cucumbers Apostichopus japonicus

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Chinese Journal of Oceanology and Limnology 2014年第1期32卷 34-46页

作者：马得友杨红生孙丽娜陈慕雁 Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of Sciences University of Chinese Academy of Sciences Ocean University of China

Sea cucumbers Apostichopus japonicus are one of the most important aquaculture species in China. Their normal body color is black to fi t their surroundings. Wild albinos are rare and hard to breed. To understand the differences between albino and normal(control) sea cucumbers at the transcriptional level, we sequenced the transcriptomes in their body-wall tissues using RNA-Seq high-throughput sequencing. Approximately 4.876 million(M) and 4.884 M 200-nucleotide-long cDNA reads were produced in the cDNA libraries derived from the body walls of albino and control samples, respectively. A total of 9 561(46.89%) putative genes were identifi ed from among the RNA-Seq reads in both libraries. After fi ltering, 837 signifi cantly differentially regulated genes were identifi ed in the albino library compared with in the control library, and 3.6% of the differentially expressed genes(DEGs) were found to have changed those more than fi ve-fold. The expression levels of 10 DEGs were checked by real-time PCR and the results were in full accord with the RNA-Seq expression trends, although the amplitude of the differences in expression levels was lower in all cases. A series of pathways were signifi cantly enriched for the DEGs. These pathways were closely related to phagocytosis, the complement and coagulation cascades, apoptosis-related diseases, cytokine-cytokine receptor interaction, and cell adhesion. The differences in gene expression and enriched pathways between the albino and control sea cucumbers offer control targets for cultivating excellent albino A. japonicus strains in the future.

关键词： albino gene expression profiling RNA-Seq real-time PCR Apostichopusjaponicus