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Ni Y, Zhang Q, Li W, Cao L, Feng R, Zhao Z, Zhao X. Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens. Fungal Biol 2024; 128:1596-1606. [PMID: 38341265 DOI: 10.1016/j.funbio.2023.12.005] [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] [Received: 09/06/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024]
Abstract
Floccularia luteovirens is one of the rare edible fungi with high nutritional value found on the Qinghai-Tibet Plateau. However, research at the molecular level on this species is currently constrained due to the lack of reliable reference genes for this species. Thirteen potential reference genes (ACT, GAPDH, EF-Tu, SAMDC, UBI, CLN1, β-TUB, γ-TUB, GTP, H3, UBC, UBC-E2, and GTPBP1) were chosen for the present study, and their expression under various abiotic conditions was investigated. Stability of gene expression was tested using GeNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder. The results showed that the most suitable reference genes for salt treatment were ACT and EF-Tu. Under drought stress, γ-TUB and UBC-E2 would be suitable for normalization. Under oxidative stress, the reference genes H3 and GAPDH worked well. Under heat stress, the reference genes EF-Tu and γ-TUB were suggested. Under extreme pH stress, UBC-E2 and H3 were appropriate reference genes. Under cadmium stress, the reference genes ACT and UBC-E2 functioned well. In different tissues, H3 and GTPBP1 were appropriate reference genes. The optimal internal reference genes when analyzing all samples were H3 and SAMDC. The expression level of HSP90 was studied to further validate the applicability of the genes identified in this study.
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Affiliation(s)
- Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Luping Cao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Zhiqiang Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Xu Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
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Su C, Xu Y. The evolving roles of radiolabeled quinones as small molecular probes in necrotic imaging. Br J Radiol 2020; 93:20200034. [PMID: 32374626 DOI: 10.1259/bjr.20200034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Necrosis plays vital roles in living organisms which is related closely with various diseases. Non-invasively necrotic imaging can be of great values in clinical decision-making, evaluation of individualized treatment responses, and prediction of patient prognosis. This narrative review will demonstrate how the evolution of quinones for necrotic imaging has been promoted by searching for their active centers. In this review, we summarized the recent developments of various quinones with the continuous simplified π-conjugated cores in necrotic imaging and speculated their possible molecular mechanisms might be attributed to their intercalations with exposed DNA in necrotic tissues. We discussed their clinical challenges of necrotic imaging with quinones and their future translation studies deserved to be explored in personalized patient treatment.
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Affiliation(s)
- Chang Su
- Office of Good Clinical Practice, The Affiliated Sir Run Run Hospital of Nanjing Medical University (the Third Affiliated Hospital of Nanjing Medical University), Nanjing 211166, Jiangsu Province, P.R.China
| | - Yan Xu
- Office of Good Clinical Practice, The Affiliated Sir Run Run Hospital of Nanjing Medical University (the Third Affiliated Hospital of Nanjing Medical University), Nanjing 211166, Jiangsu Province, P.R.China
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Li T, Hou CL, Shen XY. Efficient agrobacterium-mediated transformation of Shiraia bambusicola and activation of a specific transcription factor for hypocrellin production. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1667874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Tong Li
- College of Life Science, Capital Normal University, Beijing, PR China
| | - Cheng-Lin Hou
- College of Life Science, Capital Normal University, Beijing, PR China
| | - Xiao-Ye Shen
- College of Life Science, Capital Normal University, Beijing, PR China
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4
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Wang X, Peng F, Dong G, Sun Y, Dai X, Yang Y, Liu X, Bai Z. Identification and validation of appropriate reference genes for qRT-PCR analysis in Corynebacterium glutamicum. FEMS Microbiol Lett 2019; 365:4840241. [PMID: 29420726 DOI: 10.1093/femsle/fny030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/05/2018] [Indexed: 12/30/2022] Open
Abstract
Real-time quantitative PCR (qRT-PCR) is a fast and efficient technology for detecting gene expression levels in the study of the Corynebacterium glutamicum protein expression system, but it requires normalization to ensure the reliability of the results obtained. We selected 13 genes from the commonly used housekeeping genes and from transcriptome data as candidate reference genes. The Ct values of the 13 genes were obtained by qRT-PCR at different fermentation stages and under three stress conditions (temperature, acid and salt). The expression stability of the reference genes was evaluated by geNorm and NormFinder software. For the study of different growth stages, the most appropriate reference genes are Ncgl2772 and leua, which encode acetyl-CoA carboxylase beta subunit and 2-isopropylmalate synthase, separately. For the study of different stress factors, the optimal minimum number of reference genes is 3, with Ncgl2772, gyrb encoding DNA gyrase B and siga encoding RNA polymerase sigma factor A as the most suitable combination. Additionally, clpx and clpc, encoding ClpX and ClpC protease subunits, were used to validate the candidate reference genes. The identification of new reference genes makes qRT-PCR more convenient, and using these genes for normalization can improve the accuracy and reliability of the measurements of target gene expression levels obtained by qRT-PCR for C. glutamicum.
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Affiliation(s)
- XinYue Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feng Peng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guibin Dong
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Sun
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Dai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Ma D, Fan J, Tian Y, Jiang P, Wang J, Zhu H, Bai J. Selection of reference genes for quantitative real-time PCR normalisation in largemouth bass Micropterus salmoides fed on alternative diets. JOURNAL OF FISH BIOLOGY 2019; 95:393-400. [PMID: 31017661 DOI: 10.1111/jfb.13991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
The partial cDNA sequences of eight reference genes (actb, tuba1, gapdh58, gapdh59, eef1a1, RNA 18 s, pabpc1, ube2I) were cloned from largemouth bass Micropterus salmoides. The expression levels of these eight genes were compared in the various tissues (eye, spleen, kidney, gill, muscle, brain, liver, heart, gut and gonad) of M. salmoides fed on forage fish. The results showed that the candidate genes exhibited tissue-specific expression to various degrees and the stability ranking order was eef1a1 > tuba1 > RNA 18 s > pabpc1 > ube2I > actb > gapdh58 > gapdh59 among tissue types. Four candidate genes eef1a1, tuba1, RNA 18 s and actb were used to analyse the stability in liver tissues of largemouth bass between the forage-fish group and the formulated-feed group. The candidate genes also showed some changes in expression levels in the livers, while eef1a1 and tuba1 had the most stable expression in livers of fish fed on alternative diets within 10 candidates. So eef1a1 and tuba1 were recommended as optimal reference gene in quantitative real-time PCR analysis to normalise the expression levels of target genes in tissues and lives of the M. salmoides fed on alternative diets. In livers, the expression levels of gck normalised by eef1a1 and tuba1 showed the significant up-regulation in formulated feed group (P < 0.05) than those in forage-fish group. While sex difference has no significant effects on the expression levels of gck in both groups.
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Affiliation(s)
- Dongmei Ma
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiajia Fan
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Peng Jiang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huaping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Bai
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Qian J, Gao Y, Wáng Y, Wu Y, Wāng Y, Zhao Y, Chen H, Bao D, Xu J, Bian X. Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6125706. [PMID: 30079349 PMCID: PMC6069580 DOI: 10.1155/2018/6125706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/10/2018] [Indexed: 11/18/2022]
Abstract
Volvariella volvacea (V. volvacea), commonly referred to as Chinese (paddy straw) mushroom, is a basidiomycete with a protein-rich volva and pileus. Selecting appropriate reference genes is a crucial step in the normalization of quantitative real-time PCR data. Therefore, 12 candidate reference genes were selected from the V. volvacea transcriptome based on previous studies and then BestKeeper, geNorm, and NormFinder were used to identify reference genes stably expressed during different developmental stages and conditions. Of the 12 candidate reference genes, SPRY domain protein (SPRYp), alpha-tubulin (TUBα), cyclophilin (CYP), L-asparaginase (L-asp), and MSF1-domain-containing protein (MSF1) were the most stably expressed under different experimental conditions, while 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and beta-actin (ACTB) were the least stably expressed. This investigation not only revealed potential factors influencing the suitability of reference genes, but also identified optimal reference genes from a pool of candidate genes under a wide range of conditions.
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Affiliation(s)
- Jiang Qian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Yingnv Gao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wáng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yingying Wu
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wāng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hongyu Chen
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Jiyang Xu
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Xiaohong Bian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
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7
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Lv Y, Zhao SG, Lu G, Leung CK, Xiong ZQ, Su XW, Ma JL, Chan WY, Liu HB. Identification of reference genes for qRT-PCR in granulosa cells of healthy women and polycystic ovarian syndrome patients. Sci Rep 2017; 7:6961. [PMID: 28761164 PMCID: PMC5537281 DOI: 10.1038/s41598-017-07346-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023] Open
Abstract
Comparative gene expression analysis by qRT-PCR is commonly used to detect differentially expressed genes in studies of PCOS pathology. Impaired GC function is strongly associated with PCOS pathogenesis, and a growing body of studies has been dedicated to identifying differentially expressed genes in GCs in PCOS patients and healthy women by qRT-PCR. It is necessary to validate the expression stability of the selected reference genes across the tested samples for target gene expression normalization. We examined the variability and stability of expression of the 15 commonly used reference genes in GCs from 44 PCOS patients and 45 healthy women using the GeNorm, BestKeeper, and NormFinder statistical algorithms. We combined the rankings of the three programs to produce a final ranking based on the geometric means of their stability scores. We found that HPRT1, RPLP0, and HMBS out of 15 examined commonly used reference genes are stably expressed in GCs in both controls and PCOS patients and can be used for normalization in gene expression profiling by qRT-PCR. Future gene-expression studies should consider using these reference genes in GCs in PCOS patients for more accurate quantitation of target gene expression and data interpretation.
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Affiliation(s)
- Yue Lv
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Shi Gang Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
| | - Chi Kwan Leung
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Zhi Qiang Xiong
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Xian Wei Su
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Jin Long Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.,SDIVF R&D Centre, Hong Kong Science and Technology Parks, Hong Kong, China
| | - Wai Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China
| | - Hong Bin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250001, China. .,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong, 250001, China.
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