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Teixeira EB, Khayat AS, Assumpção PP, Casseb SM, Moreira-Nunes CA, Moreira FC. EndoGeneAnalyzer: A tool for selection and validation of reference genes. PLoS One 2024; 19:e0299993. [PMID: 38568963 PMCID: PMC10990236 DOI: 10.1371/journal.pone.0299993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024] Open
Abstract
The selection of proper reference genes is critical for accurate gene expression analysis in all fields of biological and medical research, mainly because there are many distinctions between different tissues and specimens. Given this variability, even in known classic reference genes, demands of a comprehensive analysis platform is needed to identify the most suitable genes for each study. For this purpose, we present an analysis tool for assisting in decision-making in the analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) data. EndoGeneAnalyzer, an open-source web tool for reference gene analysis in RT-qPCR studies, was used to compare the groups/conditions under investigation. This interactive application offers an easy-to-use interface that allows efficient exploration of datasets. Through statistical and stability analyses, EndoGeneAnalyzer assists in the select of the most appropriate reference gene or set of genes for each condition. It also allows researchers to identify and remove unwanted outliers. Moreover, EndoGeneAnalyzer provides a graphical interface to compare the evaluated groups, providing a visually informative differential analysis.
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Affiliation(s)
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Caroline Aquino Moreira-Nunes
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
- Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Department of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Clementino Fraga Group, Central Unity, Molecular Biology Laboratory, Fortaleza, CE, Brazil
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Silva AFB, Morais ANP, Lima LF, Ferreira ACA, Silva RF, Sá NAR, Kumar S, Oliveira AC, Alves BG, Rodrigues APR, Gastal EL, Bordignon V, Figueiredo JR. Trimethylation profile of histones H3 lysine 4 and 9 in late preantral and early antral caprine follicles grown in vivo versus in vitro in the presence of anethole. Mol Reprod Dev 2023; 90:810-823. [PMID: 37671983 DOI: 10.1002/mrd.23700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 09/07/2023]
Abstract
This study assessed the histones methylation profile (H3K4me3 and H3K9me3) in late preantral (PA) and early antral (EA) caprine follicles grown in vivo and in vitro, and the anethole effect during in vitro culture of PA follicles. Uncultured in vivo-grown follicles (PA, n = 64; EA, n = 73) were used as controls to assess the methylation profile and genes' expression related to apoptosis cascade (BAX, proapoptotic; BCL2, antiapoptotic), steroidogenesis (CYP17, CYP19A1), and demethylation (KDM1AX1, KDM1AX2, KDM3A). The isolated PA follicles (n = 174) were cultured in vitro for 6 days in α-MEM+ in either absence (control) or presence of anethole. After culture, EA follicles were evaluated for methylation, mRNA abundance, and morphometry. Follicle diameter increased after culture, regardless of treatment. The methylation profile and the mRNA abundance were similar between in vivo-grown PA and EA follicles. Anethole treatment led to higher H3K4me3 fluorescence intensity in EA follicles. The mRNA abundances of BAX, CYP17, and CYP19A1 were higher, and BCL2 and KDM3A were lower in in vitro-grown EA follicles than in vivo-grown follicles. In conclusion, in vitro follicle culture affected H3K4me3 fluorescence intensity, mRNA abundance of apoptotic genes, and steroidogenic and demethylase enzymes compared with in vivo-grown follicles.
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Affiliation(s)
- Ana F B Silva
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Ana N P Morais
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Laritza F Lima
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Anna C A Ferreira
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Renato F Silva
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Naiza A R Sá
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Satish Kumar
- Postgraduate Program in Veterinary Sciences, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Ariclécio C Oliveira
- Superior Institute of Biomedical Science, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Benner G Alves
- Postgraduate Program in Animal Bioscience, Federal University of Goiás, Jataí, Goiás, Brazil
| | - Ana P R Rodrigues
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Eduardo L Gastal
- Animal Science, School of Agricultural Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Vilceu Bordignon
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - José R Figueiredo
- Laboratory of Manipulation of Oocytes and Preantral Follicles, Faculty of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
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