Transcriptome Analysis最新文献

Revealing the Symmetry of Conifer Transcriptomes through Triplet Statistics 通过三重统计揭示针叶树转录组的对称性

Transcriptome Analysis Pub Date : 2019-09-14 DOI: 10.5772/INTECHOPEN.88696

Sadovsky Michael, Putintseva Yulia, B. Vladislav, Senashova Maria

引用次数: 0

Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility 植物比较转录组学揭示花药发育和雄性不育的功能机制和基因调控网络

Transcriptome Analysis Pub Date : 2019-07-30 DOI: 10.5772/INTECHOPEN.88318

Xiangyuan Wan, Ziwen Li

{"title":"Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility","authors":"Xiangyuan Wan, Ziwen Li","doi":"10.5772/INTECHOPEN.88318","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.88318","url":null,"abstract":"Gene transcription and transcriptional regulation are crucial biological processes in all cellular life. Through the next-generation sequencing (NGS) technology, transcriptome data from different tissues and developmental stages can be easily obtained, which provides us a powerful tool to reveal the transcriptional landscape of investigated tissue(s) at special developmental stage(s). Anther development is an important process not only for sexual plant reproduction but also for genic male sterility (GMS) used in agriculture production. Plant comparative transcriptomics has been widely used to uncover molecular mechanism of GMS. Here, we focused on researches of anther developmental process and plant GMS genes by using comparative transcriptomics method. In detail, the contents include the following: (1) we described the commonly used flowchart in comparative transcriptomics; (2) we summarized the comparative strategies used to analyze transcriptome data; (3) we presented a case study on a maize GMS gene, ZmMs33 ; (4) we described the methods and results previ-ously reported on gene co-expression and gene regulatory networks; (5) we presented the workflow of a case study on gene regulatory network reconstruction. The further development of comparative transcriptomics will provide us more powerful theoretical and application tools to investigate molecular mechanism underlying anther development and plant male sterility.","PeriodicalId":215288,"journal":{"name":"Transcriptome Analysis","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129486501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Introductory Chapter: Transcriptome Analysis 引言:转录组分析

Transcriptome Analysis Pub Date : 2019-04-08 DOI: 10.5772/INTECHOPEN.85980

M. Blumenberg

引用次数: 12

Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.) 水稻非生物胁迫转录组分析

Transcriptome Analysis Pub Date : 2019-03-30 DOI: 10.5772/INTECHOPEN.84955

Ashutosh Kumar, P. Dash

{"title":"Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.)","authors":"Ashutosh Kumar, P. Dash","doi":"10.5772/INTECHOPEN.84955","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.84955","url":null,"abstract":"Rice, a model monocot system, belongs to the family Poaceae and genus Oryza . Rice is the second largest produced cereal and staple food crop fulfilling the demand of half the world’s population. Though rice demand is growing exponentially, its production is severely affected by variable environmental changes. The various abiotic factors drastically reduce the rice plant growth and yield by affecting its different growth stages. To fulfill the growing demand of rice, it is imperative to understand its molecular responses during stresses and to develop new varieties to overcome the stresses. Earlier, the microarray experiments have been used for the identification of coexpressive gene networks during various conditions in crop plants. Though the microarray experiments provided very useful information, the unviability of genome-wide information did not provide complete information about the regulatory gene networks involved in the stress response. The advancement of molecular techniques provided breakthrough to understanding the complex regulatory gene networks and their signaling pathways during stresses. The high-throughput RNA sequencing data have opened the floodgate of transcriptome data in rice. Here we have summarized some of the transcriptome data for abiotic molecular responses in rice, which further help to understand their complex regulatory mechanism.","PeriodicalId":215288,"journal":{"name":"Transcriptome Analysis","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114453252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome 通过长读RNA测序的转录组图谱:对参考转录组的贡献

Transcriptome Analysis Pub Date : 2019-03-11 DOI: 10.5772/INTECHOPEN.84920

Dong Jin Lee, C. Hong

引用次数: 0

Single-Cell Transcriptome Analysis in Tumor Tissues 肿瘤组织单细胞转录组分析

Transcriptome Analysis Pub Date : 2019-03-09 DOI: 10.5772/INTECHOPEN.84558

S. Iwabuchi, S. Hashimoto

{"title":"Single-Cell Transcriptome Analysis in Tumor Tissues","authors":"S. Iwabuchi, S. Hashimoto","doi":"10.5772/INTECHOPEN.84558","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.84558","url":null,"abstract":"The tumor microenvironment is comprised of cancer cells and their surround-ings, including various normal cells and non-cellular components, and each tumor tissue has a distinctive microenvironment. Cancer progression is affected by different microenvironmental states, such as the heterogeneity of infiltrating immune cells. Therefore, it is necessary to understand the complex cell-to-cell interactions associated with tumor developmental stages in different tissues. Recent revolution of single-cell RNA sequencing technology can uncover the tumor microenvironment diversity. We have developed a novel strategy of single-cell transcriptome analysis: next generation 1-cell sequencing (Nx1-seq) technology, and it allows for profiling of thousands of single cells from tumor tissue. Our microwell with cell bar-code beads device can detect genes with high sensitivity, and it is easily trans-ported anywhere without any other dedicated devices. Further, the developmental cost is relatively cheaper than other single-cell RNA sequencing methods. In this study, we introduce representative application of the single-cell RNA sequencing technique in gynecological cancers, and we show the result of Nx1-seq application in human endometrioid adenocarcinoma tissue. Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.","PeriodicalId":215288,"journal":{"name":"Transcriptome Analysis","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132772735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1