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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: Database

    The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology w...

    Authors: Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman and Stephan Q. Schneider

    Citation: BMC Genomics 2018 19:618

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  2. Content type: Research article

    Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to n...

    Authors: Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang and Ming Chen

    Citation: BMC Genomics 2018 19:607

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  3. Content type: Methodology article

    The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression ...

    Authors: Stephen J. Bush, Lucy Freem, Amanda J. MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers and David A. Hume

    Citation: BMC Genomics 2018 19:594

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  4. Content type: Research article

    Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating an...

    Authors: C. Llorens, S. C. Arcos, L. Robertson, R. Ramos, R. Futami, B. Soriano, S. Ciordia, M. Careche, M. González-Muñoz, Y. Jiménez-Ruiz, N. Carballeda-Sangiao, I. Moneo, J. P. Albar, M. Blaxter and A. Navas

    Citation: BMC Genomics 2018 19:592

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  5. Content type: Research article

    The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflo...

    Authors: Jiang Chen, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yiyun Wu, Qinghua Wu and Jin Pei

    Citation: BMC Genomics 2018 19:548

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  6. Content type: Methodology article

    RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting materi...

    Authors: Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore and Zhiping Weng

    Citation: BMC Genomics 2018 19:531

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  7. Content type: Research article

    Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based...

    Authors: Robin Kosch, Julien Delarocque, Peter Claus, Stefanie C. Becker and Klaus Jung

    Citation: BMC Genomics 2018 19:530

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  8. Content type: Research article

    Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and im...

    Authors: Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds and Inanc Birol

    Citation: BMC Genomics 2018 19:536

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  9. Content type: Research article

    The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, a...

    Authors: Lixiao Du, Xincheng Zhao, Xiangzhi Liang, Xiwu Gao, Yang Liu and Guirong Wang

    Citation: BMC Genomics 2018 19:518

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  10. Content type: Research article

    Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify small RNAs as a...

    Authors: Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz and Claus O. Wilke

    Citation: BMC Genomics 2018 19:510

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  11. Content type: Methodology article

    Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipoten...

    Authors: Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom and Sandrine Dudoit

    Citation: BMC Genomics 2018 19:477

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  12. Content type: Research article

    Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynogloss...

    Authors: Yufeng Si, Haishen Wen, Yun Li, Feng He, Jifang Li, Siping Li and Huiwen He

    Citation: BMC Genomics 2018 19:464

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  13. Content type: Research article

    Iron (Fe) is an essential micronutrient for plants. Utilization of Fe deficiency-tolerant rootstock is an effective strategy to prevent Fe deficiency problems in fruit trees production. Malus halliana is an apple...

    Authors: Yan-xiu Wang, Ya Hu, Yan-fang Zhu, Abdul Wahid Baloch, Xu-mei Jia and Ai-xia Guo

    Citation: BMC Genomics 2018 19:461

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  14. Content type: Software

    Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methyla...

    Authors: Julien Richard Albert, Tasuku Koike, Hamid Younesy, Richard Thompson, Aaron B. Bogutz, Mohammad M. Karimi and Matthew C. Lorincz

    Citation: BMC Genomics 2018 19:463

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  15. Content type: Research article

    Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to iden...

    Authors: C. Peraldo-Neia, P. Ostano, G. Cavalloni, Y. Pignochino, D. Sangiolo, L. De Cecco, E. Marchesi, D. Ribero, A. Scarpa, A. M. De Rose, A. Giuliani, F. Calise, C. Raggi, P. Invernizzi, M. Aglietta, G. Chiorino…

    Citation: BMC Genomics 2018 19:440

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  16. Content type: Research article

    CCHCR1 (Coiled-Coil α-Helical Rod protein 1) is a putative psoriasis candidate gene with the risk alleles CCHCR1*WWCC and *Iso3, the latter inhibiting the translation of isoform 1. CCHCR1 was recently shown to be...

    Authors: Mari H. Tervaniemi, Shintaro Katayama, Tiina Skoog, H. Annika Siitonen, Jyrki Vuola, Kristo Nuutila, Kristiina Tammimies, Sari Suomela, Esko Kankuri, Juha Kere and Outi Elomaa

    Citation: BMC Genomics 2018 19:432

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  17. Content type: Research article

    Scylla paramamosain (Crustacea: Decapoda: Portunidae: Syclla De Hann) is a commercially important mud crab distributed along the coast of southern China and other Indo-Pacific countries (Lin Z, Hao M, Zhu D, et a...

    Authors: Huan Wang, Lei Tang, Hongling Wei, Junkai Lu, Changkao Mu and Chunlin Wang

    Citation: BMC Genomics 2018 19:421

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  18. Content type: Methodology article

    Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been ...

    Authors: Kuan Feng, Justin Costa and Jeremy S. Edwards

    Citation: BMC Genomics 2018 19:416

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  19. Content type: Research article

    Small RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next...

    Authors: Mohamed El-Mogy, Bernard Lam, Taha A. Haj-Ahmad, Shannon McGowan, Darrick Yu, Lucas Nosal, Nezar Rghei, Pam Roberts and Yousef Haj-Ahmad

    Citation: BMC Genomics 2018 19:408

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  20. Content type: Software

    Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular ch...

    Authors: Wenjie Sun, Ting Duan, Panmeng Ye, Kelie Chen, Guanling Zhang, Maode Lai and Honghe Zhang

    Citation: BMC Genomics 2018 19:405

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  21. Content type: Methodology article

    MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conv...

    Authors: Chung Wah Wu, Jared M. Evans, Shengbing Huang, Douglas W. Mahoney, Brian A. Dukek, William R. Taylor, Tracy C. Yab, Thomas C. Smyrk, Jin Jen, John B. Kisiel and David A. Ahlquist

    Citation: BMC Genomics 2018 19:401

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  22. Content type: Research article

    The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicti...

    Authors: Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée and Didier Mazel

    Citation: BMC Genomics 2018 19:373

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  23. Content type: Research article

    Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analy...

    Authors: Felix Seifert, Alexander Thiemann, Tobias A. Schrag, Dominika Rybka, Albrecht E. Melchinger, Matthias Frisch and Stefan Scholten

    Citation: BMC Genomics 2018 19:371

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  24. Content type: Research article

    Caponization results in reduced androgen levels, which leads to abdominal fat accumulation in capons. In this study, we sought to understand the molecular mechanisms behind this fat accumulation.

    Authors: Xiaoyan Cui, Huanxian Cui, Lu Liu, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2018 19:344

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  25. Content type: Research article

    337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory f...

    Authors: Longqing Sun, Genlou Sun, Chenxia Shi and Dongfa Sun

    Citation: BMC Genomics 2018 19:333

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  26. Content type: Methodology article

    Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA seque...

    Authors: Ashish Yeri, Amanda Courtright, Kirsty Danielson, Elizabeth Hutchins, Eric Alsop, Elizabeth Carlson, Michael Hsieh, Olivia Ziegler, Avash Das, Ravi V. Shah, Joel Rozowsky, Saumya Das and Kendall Van Keuren-Jensen

    Citation: BMC Genomics 2018 19:331

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  27. Content type: Methodology article

    Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable ...

    Authors: Wells W. Wu, Je-Nie Phue, Chun-Ting Lee, Changyi Lin, Lai Xu, Rong Wang, Yaqin Zhang and Rong-Fong Shen

    Citation: BMC Genomics 2018 19:326

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  28. Content type: Research article

    Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during panc...

    Authors: Zhihua Li and Rodney Rouse

    Citation: BMC Genomics 2018 19:297

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  29. Content type: Research article

    Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas ae...

    Authors: Erin E. Gill, Luisa S. Chan, Geoffrey L. Winsor, Neil Dobson, Raymond Lo, Shannan J. Ho Sui, Bhavjinder K. Dhillon, Patrick K. Taylor, Raunak Shrestha, Cory Spencer, Robert E. W. Hancock, Peter J. Unrau and Fiona S. L. Brinkman

    Citation: BMC Genomics 2018 19:223

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  30. Content type: Research article

    The anthocyanins are highly enriched in eggplants (Solanum melongena L.) with purple peel. However, our previous study showed that anthocyanins biosynthesis in eggplant cultivar ‘Lanshan Hexian’ was completely re...

    Authors: Jing Li, Yong-Jun He, Lu Zhou, Yang Liu, Mingmin Jiang, Li Ren and Huoying Chen

    Citation: BMC Genomics 2018 19:201

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    The Correction to this article has been published in BMC Genomics 2018 19:324

  31. Content type: Methodology article

    Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires ei...

    Authors: Zachary T. Herbert, Jamie P. Kershner, Vincent L. Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc…

    Citation: BMC Genomics 2018 19:199

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  32. Content type: Methodology article

    Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functio...

    Authors: Sebastian J. Teran Hidalgo and Shuangge Ma

    Citation: BMC Genomics 2018 19:198

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  33. Content type: Methodology article

    The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measuremen...

    Authors: P. Scott Pine, Steven P. Lund, Jerod R. Parsons, Lindsay K. Vang, Ashish A. Mahabal, Luca Cinquini, Sean C. Kelly, Heather Kincaid, Daniel J. Crichton, Avrum Spira, Gang Liu, Adam C. Gower, Harvey I. Pass, Chandra Goparaju, Steven M. Dubinett, Kostyantyn Krysan…

    Citation: BMC Genomics 2018 19:180

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  34. Content type: Methodology article

    Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene region...

    Authors: Bai-Han Zhu, Jun Xiao, Wei Xue, Gui-Cai Xu, Ming-Yuan Sun and Jiong-Tang Li

    Citation: BMC Genomics 2018 19:175

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  35. Content type: Research article

    RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs...

    Authors: Yaron Orenstein, Uwe Ohler and Bonnie Berger

    Citation: BMC Genomics 2018 19:154

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  36. Content type: Research article

    Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The down...

    Authors: Tian Gao, Jiang Shu and Juan Cui

    Citation: BMC Genomics 2018 19:146

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  37. Content type: Software

    Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of...

    Authors: Jackson A. Killian, Taha M. Topiwala, Alex R. Pelletier, David E. Frankhouser, Pearlly S. Yan and Ralf Bundschuh

    Citation: BMC Genomics 2018 19:139

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  38. Content type: Methodology article

    High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method would greatly expand the scope of feasible multi-site collaborations and max...

    Authors: Wanxin Wang, Lolita Penland, Ozgun Gokce, Derek Croote and Stephen R. Quake

    Citation: BMC Genomics 2018 19:140

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  39. Content type: Methodology article

    Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during ada...

    Authors: Cloelia Dard-Dascot, Delphine Naquin, Yves d’Aubenton-Carafa, Karine Alix, Claude Thermes and Erwin van Dijk

    Citation: BMC Genomics 2018 19:118

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  40. Content type: Methodology article

    Exosomes and other extracellular vesicles (EVs) have emerged as an important mechanism of cell-to-cell communication. However, previous studies either did not fully resolve what genetic materials were shuttled...

    Authors: Jialiang Yang, Jacob Hagen, Kalyani V. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stephane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev…

    Citation: BMC Genomics 2017 18:987

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  41. Content type: Methodology

    Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well estab...

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

    Citation: BMC Genomics 2017 18:985

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  42. Content type: Research article

    Transcriptome and proteome analyses on fruit pulp from the blood orange ‘Zaohong’ and the navel orange ‘twenty-first century’ were performed to study Citrus sinensis quality-related molecular changes during conse...

    Authors: Jian-hui Wang, Jian-jun Liu, Ke-ling Chen, Hong-wen Li, Jian He, Bin Guan and Li He

    Citation: BMC Genomics 2017 18:984

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  43. Content type: Methodology article

    In order to better understand the multifactorial nature of osteoporosis, animal models are utilized and compared to healthy controls. Female sheep are well established as a model for osteoporosis induced by ov...

    Authors: Felix Schulze, Deeksha Malhan, Thaqif El Khassawna, Christian Heiss, Anja Seckinger, Dirk Hose and Angela Rösen-Wolff

    Citation: BMC Genomics 2017 18:975

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  44. Content type: Research article

    Meat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the hi...

    Authors: Larissa Fernanda Simielli Fonseca, Daniele Fernanda Jovino Gimenez, Danielly Beraldo dos Santos Silva, Roger Barthelson, Fernando Baldi, Jesus Aparecido Ferro and Lucia Galvão Albuquerque

    Citation: BMC Genomics 2017 18:945

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  45. Content type: Research article

    It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals.

    Authors: Huaping Liu, Yawei Li, Jun He, Qingzhou Guan, Rou Chen, Haidan Yan, Weicheng Zheng, Kai Song, Hao Cai, You Guo, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2017 18:913

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