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Transcriptomic methods

This section covers novel experimental and analytical approaches for transcriptomic, epigenetic, and related high-throughput genomic studies. Studies which use transcriptomic and high-throughput genomic methods, but which do not present a novel methodological approach, should be submitted to the section in the journal relating to the organism studied.

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  1. Content type: Methodology article

    RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The ...

    Authors: Alberto Berral-Gonzalez, Angela L. Riffo-Campos and Guillermo Ayala

    Citation: BMC Genomics 2019 20:259

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  2. Content type: Research article

    Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, whic...

    Authors: Shuonan Duan, Binhui Liu, Yuanyuan Zhang, Guoliang Li and Xiulin Guo

    Citation: BMC Genomics 2019 20:257

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  3. Content type: Software

    The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two fi...

    Authors: Mathieu Bahin, Benoit F. Noël, Valentine Murigneux, Charles Bernard, Leila Bastianelli, Hervé Le Hir, Alice Lebreton and Auguste Genovesio

    Citation: BMC Genomics 2019 20:250

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  4. Content type: Methodology article

    Epigenetic dysregulation is involved in the etiology and progression of various human diseases. Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and ...

    Authors: Jian Zhong, Zhenqing Ye, Chad R. Clark, Samuel W. Lenz, Justin H. Nguyen, Huihuang Yan, Keith D. Robertson, Gianrico Farrugia, Zhiguo Zhang, Tamas Ordog and Jeong-Heon Lee

    Citation: BMC Genomics 2019 20:249

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  5. Content type: Research article

    Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on t...

    Authors: Annageldi Tayyrov, Claire E. Stanley, Sophie Azevedo and Markus Künzler

    Citation: BMC Genomics 2019 20:243

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  6. Content type: Methodology article

    Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield...

    Authors: Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Frank Speleman and Kaat Durinck

    Citation: BMC Genomics 2019 20:228

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  7. Content type: Research article

    Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability ...

    Authors: Shan-Shan Zhou, Zhen Xing, Hui Liu, Xian-Ge Hu, Qiong Gao, Jie Xu, Si-Qian Jiao, Kai-Hua Jia, Yu Qing Jin, Wei Zhao, Ilga Porth, Yousry A. El-Kassaby and Jian-Feng Mao

    Citation: BMC Genomics 2019 20:213

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  8. Content type: Research article

    Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell pop...

    Authors: H. L. Smith, A. Stevens, B. Minogue, S. Sneddon, L. Shaw, L. Wood, T. Adeniyi, H. Xiao, P. Lio, S. J. Kimber and D. R. Brison

    Citation: BMC Genomics 2019 20:171

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  9. Content type: Research article

    Microglia are multifunctional cells that are key players in brain development and homeostasis. Recent years have seen tremendous growth in our understanding of the role microglia play in neurodegeneration, CNS...

    Authors: Christine E. Cho, Sagar S. Damle, Edward V. Wancewicz, Swagatam Mukhopadhyay, Christopher E. Hart, Curt Mazur, Eric E. Swayze and Fredrik Kamme

    Citation: BMC Genomics 2019 20:164

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  10. Content type: Methodology article

    Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expressi...

    Authors: Xue Qing David Wang, Christopher J. F. Cameron, Denis Paquette, Dana Segal, Reid Warsaba, Mathieu Blanchette and Josée Dostie

    Citation: BMC Genomics 2019 20:162

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  11. Content type: Methodology article

    Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means o...

    Authors: Yun Zhao, Ke Wang, Wen-li Wang, Ting-ting Yin, Wei-qi Dong and Chang-jie Xu

    Citation: BMC Genomics 2019 20:160

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  12. Content type: Research article

    Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity...

    Authors: Xiaoling Zhang, Yanli Wang, Yuanyuan Yan, Hua Peng, Yun Long, Yinchao Zhang, Zhou Jiang, Peng Liu, Chaoying Zou, Huanwei Peng, Guangtang Pan and Yaou Shen

    Citation: BMC Genomics 2019 20:159

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  13. Content type: Research article

    Identifying mRNA targets of miRNAs is critical for studying gene expression regulation at the whole-genome level. Multiple computational tools have been developed to predict miRNA:mRNA interactions. Nonetheles...

    Authors: Bi Zhao and Bin Xue

    Citation: BMC Genomics 2019 20:158

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  14. Content type: Research article

    Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and co...

    Authors: Adrian C. Paskey, Kenneth G. Frey, Gary Schroth, Stephen Gross, Theron Hamilton and Kimberly A. Bishop-Lilly

    Citation: BMC Genomics 2019 20:155

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  15. Content type: Research article

    Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on...

    Authors: Bharat Bhusan Patnaik, Jong Min Chung, Hee Ju Hwang, Min Kyu Sang, Jie Eun Park, Hye Rin Min, Hang Chul Cho, Neha Dewangan, Snigdha Baliarsingh, Se Won Kang, So Young Park, Yong Hun Jo, Hong Seog Park, Wan Jong Kim, Yeon Soo Han, Jun Sang Lee…

    Citation: BMC Genomics 2019 20:154

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  16. Content type: Methodology article

    Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA’s functional versatility includes epigenetic modification, nuclear domain organization, transcriptional c...

    Authors: Sarah C. Pyfrom, Hong Luo and Jacqueline E. Payton

    Citation: BMC Genomics 2019 20:137

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  17. Content type: Research article

    Methanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newl...

    Authors: Anh Duc Nguyen, Donghyuk Kim and Eun Yeol Lee

    Citation: BMC Genomics 2019 20:130

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  18. Content type: Research article

    Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation,...

    Authors: Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny and Krzysztof Fujarewicz

    Citation: BMC Genomics 2019 20:114

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  19. Content type: Methodology article

    Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data fr...

    Authors: Wenbin Ye, Yuqi Long, Guoli Ji, Yaru Su, Pengchao Ye, Hongjuan Fu and Xiaohui Wu

    Citation: BMC Genomics 2019 20:75

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  20. Content type: Research article

    Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and acceler...

    Authors: Chen Huang, Dongliang Leng, Shixue Sun and Xiaohua Douglas Zhang

    Citation: BMC Genomics 2019 20:48

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  21. Content type: Research article

    Transcription factors (TFs) specifically bind to DNA sequences and control the expression of target genes. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamento...

    Authors: Hiroya Oka, Takaaki Kojima, Kunio Ihara, Tetsuo Kobayashi and Hideo Nakano

    Citation: BMC Genomics 2019 20:16

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  22. Content type: Research article

    3’ RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and...

    Authors: Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis and Matteo Pellegrini

    Citation: BMC Genomics 2019 20:9

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  23. Content type: Software

    Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by...

    Authors: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore and Manuel Garber

    Citation: BMC Genomics 2019 20:6

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  24. Content type: Research article

    MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in the regulation of gene expression. However, the role of miRNAs in bovine mammary gland responses to heat stress is not well u...

    Authors: Qiuling Li, Chunhong Yang, Juan Du, Baogui Zhang, Ying He, Qimeng Hu, Meiru Li, Yiming Zhang, Changfa Wang and Jifeng Zhong

    Citation: BMC Genomics 2018 19:975

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  25. Content type: Software

    New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina libr...

    Authors: Dario Romagnoli, Giulia Boccalini, Martina Bonechi, Chiara Biagioni, Paola Fassan, Roberto Bertorelli, Veronica De Sanctis, Angelo Di Leo, Ilenia Migliaccio, Luca Malorni and Matteo Benelli

    Citation: BMC Genomics 2018 19:960

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  26. Content type: Methodology article

    When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and resea...

    Authors: John R. Stevens, Jennifer S. Herrick, Roger K. Wolff and Martha L. Slattery

    Citation: BMC Genomics 2018 19:953

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  27. Content type: Research article

    Peanut is the world’s fourth largest oilseed crop that exhibits wide cultivar variations in cadmium (Cd) accumulation. To establish the mechanisms of Cd distribution and accumulation in peanut plants, eight cD...

    Authors: Rugang Yu, Yuanyuan Ma, Yue Li, Xin Li, Caifeng Liu, Xueling Du and Gangrong Shi

    Citation: BMC Genomics 2018 19:938

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  28. Content type: Research article

    The Pacific abalone, Haliotis discus hannai, is the most important cultivated abalone in China. Improving abalone muscle growth and increasing the rate of growth are important genetic improvement programs in this...

    Authors: Jianfang Huang, Xuan Luo, Miaoqin Huang, Guangmou Liu, Weiwei You and Caihuan Ke

    Citation: BMC Genomics 2018 19:915

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  29. Content type: Research article

    Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide app...

    Authors: Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecilia Maria Arraiano and Muriel Cocaign-Bousquet

    Citation: BMC Genomics 2018 19:848

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  30. Content type: Methodology article

    Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or tumor grade. Low-coverage sequencing for reporting ...

    Authors: Sangdi Lin, Chen Wang, Shabnam Zarei, Debra A. Bell, Sarah E. Kerr, George C. Runger and Jean-Pierre A. Kocher

    Citation: BMC Genomics 2018 19:841

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  31. Content type: Research article

    Antimicrobial peptides (AMPs) are multifunctional effector molecules that often combine direct antimicrobial activities with signaling or immunomodulatory functions. The skin secretions of anurans contain a va...

    Authors: Tomislav Rončević, Marco Gerdol, Francesca Spazzali, Fiorella Florian, Stjepan Mekinić, Alessandro Tossi and Alberto Pallavicini

    Citation: BMC Genomics 2018 19:827

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  32. Content type: Software

    Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, ...

    Authors: Amanda W. Ernlund, Robert J. Schneider and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:809

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  33. Content type: Research article

    Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of th...

    Authors: Luyun Ning, Zhiwei Lin, Jianwei Gu, Lu Gan, Yonghong Li, Hao Wang, Liyun Miao, Libin Zhang, Baoshan Wang and Maoteng Li

    Citation: BMC Genomics 2018 19:806

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  34. Content type: Methodology article

    Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count dat...

    Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli and Héctor Corrada Bravo

    Citation: BMC Genomics 2018 19:799

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  35. Content type: Methodology article

    Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover...

    Authors: Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang and Yudi Pawitan

    Citation: BMC Genomics 2018 19:786

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  36. Content type: Research article

    Transmissible gastroenteritis virus (TGEV) infection can activate NF-κB pathway in porcine intestinal epithelial cells and result in severe inflammation. Non-coding RNAs (ncRNAs) are not translated into protei...

    Authors: Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang and Dewen Tong

    Citation: BMC Genomics 2018 19:747

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  37. Content type: Research article

    Gray leaf spot (GLS), which is caused by the necrotrophic fungi Cercospora zeae-maydis and Cercospora zeina, is one of the most impactful diseases in maize worldwide. The aim of the present study is to identify t...

    Authors: Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Haichun Shi, Yongpei Ke and Qun Sun

    Citation: BMC Genomics 2018 19:742

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  38. Content type: Research article

    Transcription factors are essential regulators of gene expression and play critical roles in development, differentiation, and in many cancers. To carry out their regulatory programs, they must cooperate in ne...

    Authors: Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo and Kevin R. Coombes

    Citation: BMC Genomics 2018 19:738

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  39. Content type: Research article

    Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and ...

    Authors: Yuan Li, Rong-Hong Li, Ming-Xia Ran, Yan Zhang, Kai Liang, Ying-Nan Ren, Wen-Cheng He, Ming Zhang, Guang-Bin Zhou, Izhar Hyder Qazi and Chang-Jun Zeng

    Citation: BMC Genomics 2018 19:736

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  40. Content type: Research article

    RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to spl...

    Authors: Juan P. Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pío, Matthew W. B. Trotter and Angel Rubio

    Citation: BMC Genomics 2018 19:703

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  41. Content type: Research article

    Cell type-specific ribosome-pulldown has become an increasingly popular method for analysis of gene expression. It allows for expression analysis from intact tissues and monitoring of protein synthesis in vivo...

    Authors: Yang Song, Beatrice Milon, Sandra Ott, Xuechu Zhao, Lisa Sadzewicz, Amol Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar and Ronna Hertzano

    Citation: BMC Genomics 2018 19:696

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  42. Content type: Research article

    The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during co...

    Authors: Maria Ballester, Marcel Amills, Olga González-Rodríguez, Tainã F. Cardoso, Mariam Pascual, Rayner González-Prendes, Núria Panella-Riera, Isabel Díaz, Joan Tibau and Raquel Quintanilla

    Citation: BMC Genomics 2018 19:682

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  43. Content type: Software

    The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity g...

    Authors: Seokhyun Yoon, Daeseung Kim, Keunsoo Kang and Woong June Park

    Citation: BMC Genomics 2018 19:653

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  44. Content type: Research article

    Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a widely cultivated medicinal and edible crop with excellent economic and nutritional value. The development of tartary buckwheat seeds is a very complex process...

    Authors: Moyang Liu, Zhaotang Ma, Tianrun Zheng, Wenjun Sun, Yanjun Zhang, Weiqiong Jin, Junyi Zhan, Yuntao Cai, Yujia Tang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2018 19:648

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