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Uenosono Y, Kawakami R, Matsumoto S, Yamaguchi Y. Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel gene discovery. J Microbiol Methods 2023; 204:106631. [PMID: 36503828 DOI: 10.1016/j.mimet.2022.106631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
Abstract
Microorganisms in the environment can be distinguished into dominant and rare microbial species based on their genes. It is difficult to obtain genetic information derived from rare microbial species (rare genes) because of the differences in relative abundance. DNA normalization is an approach that is used to obtain genetic information derived from rare microbial species from an environmental sample. This method involves the addition of adapter sequences for the amplification, denaturation, and reassociation of the DNA fragments and single-stranded DNA (ssDNA)/double-stranded DNA (dsDNA) separation. In this method, the amount of a high-copy-number of DNA fragments and a low-copy-number of DNA fragments can be equalized. Improvements in this technique are expected to provide novel genetic information or genes in rare microbial species. However, few model experimental systems have been reported to validate the DNA normalization techniques. This study is aimed to improve the DNA normalization technique used to obtain genetic information of rare genes from rare microbial species. An experimental study was constructed with two antibiotic resistance genes, whose copy numbers differed up to a million-fold. Both genes were mixed and the mixture of DNA fragments, of high- and low-copy-number, containing these genes was normalized by separating ssDNA/dsDNA fragments using hydroxyapatite. Normalized DNA fragments were introduced into Escherichia coli and DNA normalization was evaluated by counting colonies. Moreover, we improved the method to amplify a low-copy-number of DNA fragments by the addition of adapter sequences to DNA fragments using HiDi DNA polymerase to increase the efficiency of DNA normalization. This normalization method was achieved with a 100,000-fold difference. These methods allowed for quantitative evaluation of the DNA normalization efficiency. The experimental data and methods obtained in this study are expected to improve the DNA normalization efficiency to obtain novel genetic information or genes.
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Affiliation(s)
- Yuya Uenosono
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Ryohei Kawakami
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Shogo Matsumoto
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Yoshihiro Yamaguchi
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan; Environmental Safety Center, Kumamoto University, 2-40-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
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Abstract
Hi-C has been predominately used to study the genome-wide interactions of genomes. In Hi-C experiments, it is believed that biases originating from different systematic deviations lead to extraneous variability among raw samples, and affect the reliability of downstream interpretations. As an important pipeline in Hi-C analysis, normalization seeks to remove the unwanted systematic biases; thus, a comparison between Hi-C normalization methods benefits their choice and the downstream analysis. In this article, a comprehensive comparison is proposed to investigate six Hi-C normalization methods in terms of multiple considerations. In light of comparison results, it has been shown that a cross-sample approach significantly outperforms individual sample methods in most considerations. The differences between these methods are analyzed, some practical recommendations are given, and the results are summarized in a table to facilitate the choice of the six normalization methods. The source code for the implementation of these methods is available at https://github.com/lhqxinghun/bioinformatics/tree/master/Hi-C/NormCompare.
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3
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Dual Gene Expression Analysis Identifies Factors Associated with Staphylococcus aureus Virulence in Diabetic Mice. Infect Immun 2019; 87:IAI.00163-19. [PMID: 30833333 DOI: 10.1128/iai.00163-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen of the skin. The global burden of diabetes is high, with S. aureus being a major complication of diabetic wound infections. We investigated how the diabetic environment influences S. aureus skin infection and observed an increased susceptibility to infection in mouse models of both type I and type II diabetes. A dual gene expression approach was taken to investigate transcriptional alterations in both the host and bacterium after infection. While analysis of the host response revealed only minor changes between infected control and diabetic mice, we observed that S. aureus isolated from diabetic mice had significant increases in the levels of genes associated with translation and posttranslational modification and chaperones and reductions in the levels of genes associated with amino acid transport and metabolism. One family of genes upregulated in S. aureus isolated from diabetic lesions encoded the Clp proteases, associated with the misfolded protein response. The Clp proteases were found to be partially glucose regulated as well as influencing the hemolytic activity of S. aureus Strains lacking the Clp proteases ClpX, ClpC, and ClpP were significantly attenuated in our animal model of skin infection, with significant reductions observed in dermonecrosis and bacterial burden. In particular, mutations in clpP and clpX were significantly attenuated and remained attenuated in both normal and diabetic mice. Our data suggest that the diabetic environment also causes changes to occur in invading pathogens, and one of these virulence determinants is the Clp protease system.
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Single-Cell RNA-Seq by Multiple Annealing and Tailing-Based Quantitative Single-Cell RNA-Seq (MATQ-Seq). Methods Mol Biol 2019; 1979:57-71. [PMID: 31028632 DOI: 10.1007/978-1-4939-9240-9_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Single-cell technologies have emerged as advanced tools to study various biological processes that demand the single cell resolution. To detect subtle heterogeneity in the transcriptome, high accuracy and sensitivity are still desired for single-cell RNA-seq. We describe here multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq) with ~90% capture efficiency. In addition, MATQ-seq is a total RNA assay allowing for detection of nonpolyadenylated transcripts.
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Miller PR, Taylor RM, Tran BQ, Boyd G, Glaros T, Chavez VH, Krishnakumar R, Sinha A, Poorey K, Williams KP, Branda SS, Baca JT, Polsky R. Extraction and biomolecular analysis of dermal interstitial fluid collected with hollow microneedles. Commun Biol 2018; 1:173. [PMID: 30374463 PMCID: PMC6197253 DOI: 10.1038/s42003-018-0170-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 09/14/2018] [Indexed: 12/30/2022] Open
Abstract
Dermal interstitial fluid (ISF) is an underutilized information-rich biofluid potentially useful in health status monitoring applications whose contents remain challenging to characterize. Here, we present a facile microneedle approach for dermal ISF extraction with minimal pain and no blistering for human subjects and rats. Extracted ISF volumes were sufficient for determining transcriptome, and proteome signatures. We noted similar profiles in ISF, serum, and plasma samples, suggesting that ISF can be a proxy for direct blood sampling. Dynamic changes in RNA-seq were recorded in ISF from induced hypoxia conditions. Finally, we report the first isolation and characterization, to our knowledge, of exosomes from dermal ISF. The ISF exosome concentration is 12-13 times more enriched when compared to plasma and serum and represents a previously unexplored biofluid for exosome isolation. This minimally invasive extraction approach can enable mechanistic studies of ISF and demonstrates the potential of ISF for real-time health monitoring applications.
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Affiliation(s)
- Philip R Miller
- Nano and Micro Sensors, Sandia National Laboratories, Albuquerque, NM, 87185, USA
| | - Robert M Taylor
- Department of Emergency Medicine, The University of New Mexico, Albuquerque, NM, 87131, USA
| | - Bao Quoc Tran
- Excet Inc., 6225 Brandon Ave, Suite 360, Springfield, VA, 22150, USA
| | - Gabrielle Boyd
- Excet Inc., 6225 Brandon Ave, Suite 360, Springfield, VA, 22150, USA
| | - Trevor Glaros
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Edgewood, MD, 21010, USA
| | - Victor H Chavez
- Nano and Micro Sensors, Sandia National Laboratories, Albuquerque, NM, 87185, USA
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Anupama Sinha
- Systems Biology, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Kunal Poorey
- Systems Biology, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Kelly P Williams
- Systems Biology, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Steven S Branda
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Justin T Baca
- Department of Emergency Medicine, The University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Ronen Polsky
- Nano and Micro Sensors, Sandia National Laboratories, Albuquerque, NM, 87185, USA.
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6
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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Bent ZW, Poorey K, LaBauve AE, Hamblin R, Williams KP, Meagher RJ. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing. PLoS One 2016; 11:e0168788. [PMID: 28002481 PMCID: PMC5176299 DOI: 10.1371/journal.pone.0168788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023] Open
Abstract
When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich for pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.
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Affiliation(s)
- Zachary W. Bent
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail: (ZWB); (RJM)
| | - Kunal Poorey
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Annette E. LaBauve
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Rachelle Hamblin
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Kelly P. Williams
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Robert J. Meagher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail: (ZWB); (RJM)
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8
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Matteau D, Rodrigue S. Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5'-Rapid Amplification of cDNA Ends (5'-RACE). Methods Mol Biol 2016; 1334:143-59. [PMID: 26404148 DOI: 10.1007/978-1-4939-2877-4_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Transcription start sites are commonly used to locate promoter elements in bacterial genomes. TSS were previously studied one gene at a time, often through 5'-rapid amplification of cDNA ends (5'-RACE). This technique has now been adapted for high-throughput sequencing and can be used to precisely identify TSS in a genome-wide fashion for practically any bacterium, which greatly contributes to our understanding of gene regulatory networks in microorganisms.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
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Abstract
Y. pestis exhibits dramatically different traits of pathogenicity and transmission, albeit their close genetic relationship with its ancestor-Y. pseudotuberculosis, a self-limiting gastroenteric pathogen. Y. pestis is evolved into a deadly pathogen and transmitted to mammals and/or human beings by infected flea biting or directly contacting with the infected animals. Various kinds of environmental changes are implicated into its complex life cycle and pathogenesis. Dynamic regulation of gene expression is critical for environmental adaptation or survival, primarily reflected by genetic regulation mediated by transcriptional factors and small regulatory RNAs at the transcriptional and posttranscriptional level, respectively. The effects of genetic regulation have been shown to profoundly influence Y. pestis physiology and pathogenesis such as stress resistance, biofilm formation, intracellular survival, and replication. In this chapter, we mainly summarize the progresses on popular methods of genetic regulation and on regulatory patterns and consequences of many key transcriptional and posttranscriptional regulators, with a particular emphasis on how genetic regulation influences the biofilm and virulence of Y. pestis.
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Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol 2015; 11:e1004393. [PMID: 26248053 PMCID: PMC4527835 DOI: 10.1371/journal.pcbi.1004393] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki.
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Affiliation(s)
- Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Nicholas C. Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Benjamin J. Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Obi L. Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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11
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Transcriptomic Analysis of Yersinia enterocolitica Biovar 1B Infecting Murine Macrophages Reveals New Mechanisms of Extracellular and Intracellular Survival. Infect Immun 2015; 83:2672-85. [PMID: 25895974 DOI: 10.1128/iai.02922-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/10/2015] [Indexed: 11/20/2022] Open
Abstract
Yersinia enterocolitica is typically considered an extracellular pathogen; however, during the course of an infection, a significant number of bacteria are stably maintained within host cell vacuoles. Little is known about this population and the role it plays during an infection. To address this question and to elucidate the spatially and temporally dynamic gene expression patterns of Y. enterocolitica biovar 1B through the course of an in vitro infection, transcriptome sequencing and differential gene expression analysis of bacteria infecting murine macrophage cells were performed under four distinct conditions. Bacteria were first grown in a nutrient-rich medium at 26 °C to establish a baseline of gene expression that is unrelated to infection. The transcriptomes of these bacteria were then compared to bacteria grown in a conditioned cell culture medium at 37 °C to identify genes that were differentially expressed in response to the increased temperature and medium but not in response to host cells. Infections were then performed, and the transcriptomes of bacteria found on the extracellular surface and intracellular compartments were analyzed individually. The upregulated genes revealed potential roles for a variety of systems in promoting intracellular virulence, including the Ysa type III secretion system, the Yts2 type II secretion system, and the Tad pilus. It was further determined that mutants of each of these systems had decreased virulence while infecting macrophages. Overall, these results reveal the complete set of genes expressed by Y. enterocolitica in response to infection and provide the groundwork for future virulence studies.
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Archer SK, Shirokikh NE, Preiss T. Probe-Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA-Seq Libraries. ACTA ACUST UNITED AC 2015; 85:11.15.1-11.15.36. [PMID: 25827346 DOI: 10.1002/0471142905.hg1115s85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Most applications for RNA-seq require the depletion of abundant transcripts to gain greater coverage of the underlying transcriptome. The sequences to be targeted for depletion depend on application and species and in many cases may not be supported by commercial depletion kits. This unit describes a method for generating RNA-seq libraries that incorporates probe-directed degradation (PDD), which can deplete any unwanted sequence set, with the low-bias split-adapter method of library generation (although many other library generation methods are in principle compatible). The overall strategy is suitable for applications requiring customized sequence depletion or where faithful representation of fragment ends and lack of sequence bias is paramount. We provide guidelines to rapidly design specific probes against the target sequence, and a detailed protocol for library generation using the split-adapter method including several strategies for streamlining the technique and reducing adapter dimer content.
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Affiliation(s)
- Stuart K Archer
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Present address: Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia.,These authors contributed equally to this work
| | - Nikolay E Shirokikh
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Present address: Moscow Regional State Institute of Humanities and Social Studies, Ministry of Education of Moscow Region, Kolomna, Moscow Region, Russia.,These authors contributed equally to this work
| | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales, Australia
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13
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Gagic D, Maclean PH, Li D, Attwood GT, Moon CD. Improving the genetic representation of rare taxa within complex microbial communities using
DNA
normalization methods. Mol Ecol Resour 2014; 15:464-76. [DOI: 10.1111/1755-0998.12321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/28/2014] [Accepted: 08/13/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Dragana Gagic
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | | | - Dong Li
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | - Graeme T. Attwood
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
| | - Christina D. Moon
- AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand
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14
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Archer SK, Shirokikh NE, Preiss T. Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage. BMC Genomics 2014; 15:401. [PMID: 24886553 PMCID: PMC4045971 DOI: 10.1186/1471-2164-15-401] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major hurdle to transcriptome profiling by deep-sequencing technologies is that abundant transcripts, such as rRNAs, can overwhelm the libraries, severely reducing transcriptome-wide coverage. Methods for depletion of such unwanted sequences typically require treatment of RNA samples prior to library preparation, are costly and not suited to unusual species and applications. Here we describe Probe-Directed Degradation (PDD), an approach that employs hybridisation to DNA oligonucleotides at the single-stranded cDNA library stage and digestion with Duplex-Specific Nuclease (DSN). RESULTS Targeting Saccharomyces cerevisiae rRNA sequences in Illumina HiSeq libraries generated by the split adapter method we show that PDD results in efficient removal of rRNA. The probes generate extended zones of depletion as a function of library insert size and the requirements for DSN cleavage. Using intact total RNA as starting material, probes can be spaced at the minimum anticipated library size minus 20 nucleotides to achieve continuous depletion. No off-target bias is detectable when comparing PDD-treated with untreated libraries. We further provide a bioinformatics tool to design suitable PDD probe sets. CONCLUSION We find that PDD is a rapid procedure that results in effective and specific depletion of unwanted sequences from deep-sequencing libraries. Because PDD acts at the cDNA stage, handling of fragile RNA samples can be minimised and it should further be feasible to remediate existing libraries. Importantly, PDD preserves the original RNA fragment boundaries as is required for nucleotide-resolution footprinting or base-cleavage studies. Finally, as PDD utilises unmodified DNA oligonucleotides it can provide a low-cost option for large-scale projects, or be flexibly customised to suit different depletion targets, sample types and organisms.
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Affiliation(s)
| | | | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.
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15
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Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T. Next-generation technologies and data analytical approaches for epigenomics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:155-70. [PMID: 24327356 DOI: 10.1002/em.21841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 05/18/2023]
Abstract
Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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16
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Jebrail MJ, Sinha A, Vellucci S, Renzi RF, Ambriz C, Gondhalekar C, Schoeniger JS, Patel KD, Branda SS. World-to-Digital-Microfluidic Interface Enabling Extraction and Purification of RNA from Human Whole Blood. Anal Chem 2014; 86:3856-62. [DOI: 10.1021/ac404085p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mais J. Jebrail
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Anupama Sinha
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Samantha Vellucci
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Ronald F. Renzi
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Cesar Ambriz
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Carmen Gondhalekar
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Joseph S. Schoeniger
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Kamlesh D. Patel
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Steven S. Branda
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
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17
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Olsvik PA, Vikeså V, Lie KK, Hevrøy EM. Transcriptional responses to temperature and low oxygen stress in Atlantic salmon studied with next-generation sequencing technology. BMC Genomics 2013; 14:817. [PMID: 24261939 PMCID: PMC4046827 DOI: 10.1186/1471-2164-14-817] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/14/2013] [Indexed: 01/08/2023] Open
Abstract
Background Warmer seawater as a result of climate change may impose environmental challenges for Atlantic salmon aquaculture in its southernmost geographic range. Seawater temperatures above optimal level for growth may be reached in the warmest summer weeks. Caged fish can experience temperature and low oxygen saturation stress during such episodes, raising fish welfare and productivity concerns. In this work we compare the transcriptional responses in Atlantic salmon exposed to chronic high temperature (19°C) and low oxygen saturation (4-5 mg/L) stress. Results We used next-generation sequencing and RT-qPCR to screen for effects, and focused on growth regulation and oxidative stress in fish exposed to sub-optimal conditions. Both prolonged temperature (45 days) and low oxygen (120 days) stress had a significant negative effect on growth. The main effect of heat stress appears to be a general reduced transcriptional rate in salmon liver, while mechanisms typically associated with responses induced by chemical drugs were stimulated. Heat stress significantly down-regulated several transcripts encoding proteins involved in the protection against oxidative stress, including CuZn SOD, Mn SOD, GPx1 and GR, as well as additional stress markers HIF1A, CYP1A, MTOR and PSMC2 (RT-qPCR data). In salmon held at low oxygen concentration for four months protein ubiquitination (protein catabolism) was the most strongly affected pathway. According to the RT-qPCR data, low oxygen stress significantly up-regulated the transcriptional levels of IGFBP1B and down-regulated the levels of GR. Pathway analysis suggests that high temperature and low oxygen saturation stress affects many similar mechanisms in Atlantic salmon. Based on the gene lists, six out of the top ten predicted upstream transcriptional regulators, 1,2-dithiol-3-thione sirolimus, CD437, 5-fluorouracil, HNF4A and NFE2L2, were similar between the two treatments. Conclusions In conclusion, temperature and low oxygen saturation stress affect many identical mechanisms in liver cells resulting in a metabolic depression, but these effects are not necessarily mediated through altered transcription of the same genes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-817) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pål A Olsvik
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway.
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Norton N, Sun Z, Asmann YW, Serie DJ, Necela BM, Bhagwate A, Jen J, Eckloff BW, Kalari KR, Thompson KJ, Carr JM, Kachergus JM, Geiger XJ, Perez EA, Thompson EA. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors. PLoS One 2013; 8:e81925. [PMID: 24278466 PMCID: PMC3838386 DOI: 10.1371/journal.pone.0081925] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlations of >0.94 and >0.80 with NanoString and ScriptSeq protocols, respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes) and ScriptSeq whole transcriptome protocols respectively, p<2x10(-16). Specifically for lincRNAs, we observed superb Pearson correlation (0.988) between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads). Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transcriptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol performed particularly well for lincRNA expression from FFPE libraries, but detection of eSNV and fusion transcripts was less sensitive.
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Affiliation(s)
- Nadine Norton
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America
- *
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Yan W. Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Daniel J. Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Brian M. Necela
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Aditya Bhagwate
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jin Jen
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Bruce W. Eckloff
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krishna R. Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kevin J. Thompson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jennifer M. Carr
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Jennifer M. Kachergus
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Xochiquetzal J. Geiger
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Edith A. Perez
- Department of Medicine, Mayo Clinic, Jacksonville, Florida, United States of America
| | - E. Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America
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Bent ZW, Brazel DM, Tran-Gyamfi MB, Hamblin RY, VanderNoot VA, Branda SS. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages. PLoS One 2013; 8:e77834. [PMID: 24155975 PMCID: PMC3796476 DOI: 10.1371/journal.pone.0077834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq) to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.
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Affiliation(s)
- Zachary W. Bent
- Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| | - David M. Brazel
- Sandia National Laboratories, Livermore, California, United States of America
| | - Mary B. Tran-Gyamfi
- Sandia National Laboratories, Livermore, California, United States of America
| | - Rachelle Y. Hamblin
- Sandia National Laboratories, Livermore, California, United States of America
| | | | - Steven S. Branda
- Sandia National Laboratories, Livermore, California, United States of America
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Langevin SA, Bent ZW, Solberg OD, Curtis DJ, Lane PD, Williams KP, Schoeniger JS, Sinha A, Lane TW, Branda SS. Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material. RNA Biol 2013; 10:502-15. [PMID: 23558773 PMCID: PMC3710357 DOI: 10.4161/rna.24284] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows.
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Affiliation(s)
- Stanley A Langevin
- Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, USA
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21
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Enriching pathogen transcripts from infected samples: a capture-based approach to enhanced host-pathogen RNA sequencing. Anal Biochem 2013; 438:90-6. [PMID: 23535274 DOI: 10.1016/j.ab.2013.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/22/2023]
Abstract
To fully understand the interactions of a pathogen with its host, it is necessary to analyze the RNA transcripts of both the host and pathogen throughout the course of an infection. Although this can be accomplished relatively easily on the host side, the analysis of pathogen transcripts is complicated by the overwhelming amount of host RNA isolated from an infected sample. Even with the read depth provided by second-generation sequencing, it is extremely difficult to get enough pathogen reads for an effective gene-level analysis. In this study, we describe a novel capture-based technique and device that considerably enriches for pathogen transcripts from infected samples. This versatile method can, in principle, enrich for any pathogen in any infected sample. To test the technique's efficacy, we performed time course tissue culture infections using Rift Valley fever virus and Francisella tularensis. At each time point, RNA sequencing (RNA-Seq) was performed and the results of the treated samples were compared with untreated controls. The capture of pathogen transcripts, in all cases, led to more than an order of magnitude enrichment of pathogen reads, greatly increasing the number of genes hit, the coverage of those genes, and the depth at which each transcript was sequenced.
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Stewart FJ. Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine Plankton. Methods Enzymol 2013; 531:187-218. [DOI: 10.1016/b978-0-12-407863-5.00010-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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