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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 PMCID: PMC11188175 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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2
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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3
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Ogi DA, Jin S. Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine. Cells 2023; 12:1442. [PMID: 37408278 DOI: 10.3390/cells12101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 07/07/2023] Open
Abstract
Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing cellular differentiation based on promoting the expression of specific genes. It has also been utilized to determine the specific cell type. This review highlights RNAseq techniques, tools for RNAseq data interpretation, RNAseq data analytic methods and their utilities, and transcriptomics-enabled human stem cell differentiation. In addition, the review outlines the potential benefits of the transcriptomics-aided discovery of intrinsic factors influencing stem cell lineage commitment, transcriptomics applied to disease physiology studies using patients' induced pluripotent stem cell (iPSC)-derived cells for regenerative medicine, and the future outlook on the technology and its implementation.
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Affiliation(s)
- Derek A Ogi
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
- Center of Biomanufacturing for Regenerative Medicine, State University of New York at Binghamton, Binghamton, NY 13902, USA
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4
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Schreibing F, Anslinger TM, Kramann R. Fibrosis in Pathology of Heart and Kidney: From Deep RNA-Sequencing to Novel Molecular Targets. Circ Res 2023; 132:1013-1033. [PMID: 37053278 DOI: 10.1161/circresaha.122.321761] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Diseases of the heart and the kidney, including heart failure and chronic kidney disease, can dramatically impair life expectancy and the quality of life of patients. The heart and kidney form a functional axis; therefore, functional impairment of 1 organ will inevitably affect the function of the other. Fibrosis represents the common final pathway of diseases of both organs, regardless of the disease entity. Thus, inhibition of fibrosis represents a promising therapeutic approach to treat diseases of both organs and to resolve functional impairment. However, despite the growing knowledge in this field, the exact pathomechanisms that drive fibrosis remain elusive. RNA-sequencing approaches, particularly single-cell RNA-sequencing, have revolutionized the investigation of pathomechanisms at a molecular level and facilitated the discovery of disease-associated cell types and mechanisms. In this review, we give a brief overview over the evolution of RNA-sequencing techniques, summarize most recent insights into the pathogenesis of heart and kidney fibrosis, and discuss how transcriptomic data can be used, to identify new drug targets and to develop novel therapeutic strategies.
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Affiliation(s)
- Felix Schreibing
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Teresa M Anslinger
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Division of Nephrology and Clinical Immunology (F.S., T.M.A., R.K.), RWTH Aachen University, Medical Faculty, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands (R.K.)
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5
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Nguyen BD, Stevens BL, Elson DJ, Finlay D, Gamble J, Kopparapu P, Tanguay RL, Buermeyer AB, Kerkvliet NI, Kolluri SK. 11-Cl-BBQ, a select modulator of AhR-regulated transcription, suppresses lung cancer cell growth via activation of p53 and p27 Kip1. FEBS J 2023; 290:2064-2084. [PMID: 36401795 PMCID: PMC10807707 DOI: 10.1111/febs.16683] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/01/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor and functions as a tumour suppressor in different cancer models. In the present study, we report detailed characterization of 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ) as a select modulator of AhR-regulated transcription (SMAhRT) with anti-cancer actions. Treatment of lung cancer cells with 11-Cl-BBQ induced potent and sustained AhR-dependent anti-proliferative effects by promoting G1 phase cell cycle arrest. Investigation of 11-Cl-BBQ-induced transcription in H460 cells with or without the AhR expression by RNA-sequencing revealed activation of p53 signalling. In addition, 11-Cl-BBQ suppressed multiple pathways involved in DNA replication and increased expression of cyclin-dependent kinase inhibitors, including p27Kip1 , in an AhR-dependent manner. CRISPR/Cas9 knockout of individual genes revealed the requirement for both p53 and p27Kip1 for the AhR-mediated anti-proliferative effects. Our results identify 11-Cl-BBQ as a potential lung cancer therapeutic, highlight the feasibility of targeting AhR and provide important mechanistic insights into AhR-mediated-anticancer actions.
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Affiliation(s)
- Bach D. Nguyen
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Brenna L. Stevens
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Daniel J. Elson
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John Gamble
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Prasad Kopparapu
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robyn L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
| | - Andrew B. Buermeyer
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Nancy I. Kerkvliet
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Siva K. Kolluri
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
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6
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Nguyen MH, Nguyen HN, Vu TN. Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data. BMC Genomics 2022; 23:106. [PMID: 35135477 PMCID: PMC8822704 DOI: 10.1186/s12864-022-08329-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022] Open
Abstract
Background Circular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological functions and potential biomarkers of human diseases. Most of the current circRNA detection methods from RNA-sequencing (RNA-Seq) data utilize the mapping information of paired-end (PE) reads to eliminate false positives. However, much of the practical RNA-Seq data such as cross-linking immunoprecipitation sequencing (CLIP-Seq) data usually contain single-end (SE) reads. It is not clear how well these tools perform on SE RNA-Seq data. Results In this study, we present a systematic evaluation of six advanced RNA-based methods and two CLIP-Seq based methods for detecting circRNAs from SE RNA-Seq data. The performances of the methods are rigorously assessed based on precision, sensitivity, F1 score, and true discovery rate. We investigate the impacts of read length, false positive ratio, sequencing depth and PE mapping information on the performances of the methods using simulated SE RNA-Seq simulated datasets. The real datasets used in this study consist of four experimental RNA-Seq datasets with ≥100bp read length and 124 CLIP-Seq samples from 45 studies that contain mostly short-read (≤50bp) RNA-Seq data. The simulation study shows that the sensitivities of most of the methods can be improved by increasing either read length or sequencing depth, and that the levels of false positive rates significantly affect the precision of all methods. Furthermore, the PE mapping information can improve the method’s precision but can not always guarantee the increase of F1 score. Overall, no method is dominant for all SE RNA-Seq data. The RNA-based methods perform better for the long-read datasets but are worse for the short-read datasets. In contrast, the CLIP-Seq based methods outperform the RNA-Seq based methods for all the short-read samples. Combining the results of these methods can significantly improve precision in the CLIP-Seq data. Conclusions The results provide a systematic evaluation of circRNA detection methods on SE RNA-Seq data that would facilitate researchers’ strategies in circRNA analysis. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08329-7).
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Affiliation(s)
- Manh Hung Nguyen
- Information Technology Institute, Vietnam National University in Hanoi, Hanoi, Vietnam.,University of Engineering and Technology, Vietnam National University in Hanoi, Hanoi, Vietnam
| | - Ha-Nam Nguyen
- Information Technology Institute, Vietnam National University in Hanoi, Hanoi, Vietnam.,The Vietnam Institute for Advanced Study in Mathematics, Hanoi, Vietnam
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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7
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Signal B, Kahlke T. how_are_we_stranded_here: quick determination of RNA-Seq strandedness. BMC Bioinformatics 2022; 23:49. [PMID: 35065593 PMCID: PMC8783475 DOI: 10.1186/s12859-022-04572-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022] Open
Abstract
Background Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. Results To address these issues, we developed how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data. Testing on both simulated and real RNA-Sequencing reads showed that it correctly measures strandedness, and measures outside the normal range may indicate sample contamination. Conclusions how_are_we_stranded_here is fast and user friendly, making it easy to implement in quality control pipelines prior to analysing RNA-Sequencing data. how_are_we_stranded_here is freely available at https://github.com/betsig/how_are_we_stranded_here. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04572-7.
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8
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Goll JB, Bosinger SE, Jensen TL, Walum H, Grimes T, Tharp GK, Natrajan MS, Blazevic A, Head RD, Gelber CE, Steenbergen KJ, Patel NB, Sanz P, Rouphael NG, Anderson EJ, Mulligan MJ, Hoft DF. The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies. Front Immunol 2022; 13:1093242. [PMID: 36741404 PMCID: PMC9893923 DOI: 10.3389/fimmu.2022.1093242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Over the last decade, the field of systems vaccinology has emerged, in which high throughput transcriptomics and other omics assays are used to probe changes of the innate and adaptive immune system in response to vaccination. The goal of this study was to benchmark key technical and analytical parameters of RNA sequencing (RNA-seq) in the context of a multi-site, double-blind randomized vaccine clinical trial. Methods We collected longitudinal peripheral blood mononuclear cell (PBMC) samples from 10 subjects before and after vaccination with a live attenuated Francisella tularensis vaccine and performed RNA-Seq at two different sites using aliquots from the same sample to generate two replicate datasets (5 time points for 50 samples each). We evaluated the impact of (i) filtering lowly-expressed genes, (ii) using external RNA controls, (iii) fold change and false discovery rate (FDR) filtering, (iv) read length, and (v) sequencing depth on differential expressed genes (DEGs) concordance between replicate datasets. Using synthetic mRNA spike-ins, we developed a method for empirically establishing minimal read-count thresholds for maintaining fold change accuracy on a per-experiment basis. We defined a reference PBMC transcriptome by pooling sequence data and established the impact of sequencing depth and gene filtering on transcriptome representation. Lastly, we modeled statistical power to detect DEGs for a range of sample sizes, effect sizes, and sequencing depths. Results and Discussion Our results showed that (i) filtering lowly-expressed genes is recommended to improve fold-change accuracy and inter-site agreement, if possible guided by mRNA spike-ins (ii) read length did not have a major impact on DEG detection, (iii) applying fold-change cutoffs for DEG detection reduced inter-set agreement and should be used with caution, if at all, (iv) reduction in sequencing depth had a minimal impact on statistical power but reduced the identifiable fraction of the PBMC transcriptome, (v) after sample size, effect size (i.e. the magnitude of fold change) was the most important driver of statistical power to detect DEG. The results from this study provide RNA sequencing benchmarks and guidelines for planning future similar vaccine studies.
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Affiliation(s)
- Johannes B Goll
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Steven E Bosinger
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States.,Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Travis L Jensen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Hasse Walum
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Tyler Grimes
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Gregory K Tharp
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Muktha S Natrajan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Azra Blazevic
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Richard D Head
- McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Casey E Gelber
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Kristen J Steenbergen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Nirav B Patel
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Patrick Sanz
- Office of Biodefense, Research Resources and Translational Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Nadine G Rouphael
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States
| | - Evan J Anderson
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Mark J Mulligan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,New York University Vaccine Center, New York, NY, United States
| | - Daniel F Hoft
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis, MO, United States
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9
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Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, Kakhki MP, Raine A, Needhamsen M, Jagodic M. Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Epigenetics 2021; 17:1195-1204. [PMID: 34709110 PMCID: PMC9542412 DOI: 10.1080/15592294.2021.1997406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1–10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.
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Affiliation(s)
- Yanan Han
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Galina Yurevna Zheleznyakova
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
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10
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Hounkpe BW, Chenou F, de Lima F, De Paula E. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Nucleic Acids Res 2021; 49:D947-D955. [PMID: 32663312 PMCID: PMC7778946 DOI: 10.1093/nar/gkaa609] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
Housekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping and Reference Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2158 human HK transcripts from 2176 HK genes and 3024 mouse HK transcripts from 3277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with a regulatory elements resource from Epiregio server.
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Affiliation(s)
| | - Francine Chenou
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - Franciele de Lima
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - Erich Vinicius De Paula
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
- Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
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