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. Research article

    Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

    RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kit...

    Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam and Marc R. Wilkins

    BMC Genomics 2017 18:399

    Published on: 23 May 2017

  2. Research Article

    Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

    Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time poi...

    Han Rauwerda, Johanna F. B. Pagano, Wim C. de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P. Spaink and Timo M. Breit

    BMC Genomics 2017 18:287

    Published on: 11 April 2017

  3. Software

    Detect tissue heterogeneity in gene expression data with BioQC

    Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretati...

    Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Ines Pomposiello and Laura Badi

    BMC Genomics 2017 18:277

    Published on: 4 April 2017

  4. Research article

    Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage

    We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched con...

    Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A. Kyrtopoulos, Ingvar A. Bergdahl, Ann-Sofie Johansson, Dennie D.G.A.J. Hebels, Theo M.C.M. de Kok, Paolo Vineis and Roel C.H. Vermeulen

    BMC Genomics 2017 18:239

    Published on: 20 March 2017

  5. Research article

    Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

    Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible ...

    Vincent Doublet, Yvonne Poeschl, Andreas Gogol-Döring, Cédric Alaux, Desiderato Annoscia, Christian Aurori, Seth M. Barribeau, Oscar C. Bedoya-Reina, Mark J. F. Brown, James C. Bull, Michelle L. Flenniken, David A. Galbraith, Elke Genersch, Sebastian Gisder, Ivo Grosse, Holly L. Holt…

    BMC Genomics 2017 18:207

    Published on: 2 March 2017

    The Erratum to this article has been published in BMC Genomics 2017 18:256

  6. Research article

    Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

    While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribos...

    Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim and Siegfried Scherer

    BMC Genomics 2017 18:216

    Published on: 28 February 2017

  7. Research article

    Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress

    Drought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance r...

    Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, Ram Sewak Singh Tomar, Ashish Kumar Chaturvedi, Kishor Gaikwad and Madan Pal

    BMC Genomics 2017 18:206

    Published on: 27 February 2017

  8. Research article

    Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection

    The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic...

    Libo He, Aidi Zhang, Pengfei Chu, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu and Yaping Wang

    BMC Genomics 2017 18:195

    Published on: 20 February 2017

  9. Research article

    Improved annotation with de novo transcriptome assembly in four social amoeba species

    Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcri...

    Reema Singh, Hajara M. Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J. Barton, Pauline Schaap and Christian Cole

    BMC Genomics 2017 18:120

    Published on: 31 January 2017

  10. Software

    Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems

    2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute le...

    Stephenie D. Prokopec, Kathleen E. Houlahan, Ren X. Sun, John D. Watson, Cindy Q. Yao, Jamie Lee, Christine P’ng, Renee Pang, Alexander H. Wu, Lauren C. Chong, Ashley B. Smith, Nicholas J. Harding, Ivy D. Moffat, Jere Lindén, Sanna Lensu, Allan B. Okey…

    BMC Genomics 2017 18:78

    Published on: 13 January 2017

  11. Methodology article

    Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data

    Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mamma...

    Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Chun-Chi Liu and Jeremy J.W. Chen

    BMC Genomics 2017 18:61

    Published on: 10 January 2017

  12. Research

    Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium

    Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties...

    Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee and Laiq ur Rahman

    BMC Genomics 2017 18:54

    Published on: 9 January 2017

  13. Methodology article

    The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq

    Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome’s limitations in describing higher functional phenotypes and protein events. Perhaps the mos...

    Quin F. Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes…

    BMC Genomics 2017 18:53

    Published on: 7 January 2017

  14. Research Article

    De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

    The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging insect pest of corn in Asia. However, the lack of genome or transcriptome information heavily hinders our further understandi...

    Li Cui, Changhui Rui, Daibin Yang, Zhenying Wang and Huizhu Yuan

    BMC Genomics 2017 18:20

    Published on: 5 January 2017

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