Contents lists available at ScienceDirect International Journal of Biochemistry and Cell Biology journal homepage: www.elsevier.com/locate/biocel Comparative analysis of single-cell parallel sequencing approaches in oocyte application Yan Qian a , Jinyue Liao a , Ashley Hoi Ching Suen a , Annie Wing Tung Lee a , Hoi Sze Chung b , Nelson Leung Sang Tang c , King Lau Chow d , Qin Cao e , Yuk Lap Yip e , Tak Yeung Leung b , Wai-Yee Chan a , David Yiu Leung Chan b , Tin Chiu Li b , Tin-Lap Lee a, ⁎ a Developmental and Regenerative Biology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong Special Administrative Region, China b DepartmentofObstetricsandGynaecology,TheChineseUniversityofHongKong,PrinceofWalesHospital,Shatin,N.T.,HongKongSpecialAdministrativeRegion,China c Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong Special Administrative Region, China d Division of Life Science, Hong Kong University of Science and Technology, Shatin, N.T., Hong Kong Special Administrative Region, China e Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong Special Administrative Region, China ARTICLE INFO Keywords: Single cell parallel sequencing Oocyte RNA-seq Reduced representation bisulfte sequencing Whole genome bisulfte sequencing ABSTRACT Single-cell parallel sequencing allows us to explore how genetic and epigenetic variations correlate of gene expression in the same cell. Beads-based approach and non-beads-based approach are the two present methods to separate DNA and RNA from the same cell. However, systematic diference between the two methods are lacking. In our study, we compared the performances of the two methods using transcriptome and methylome profles generated simultaneously from single mouse oocytes. Our results showed that the beads-based approach could capture maximum quantity of mRNA but loss of DNA was inevitable, while the non-beads-based approach could obtain more DNA due to the undamaged nucleus obtained but at a cost of partial loss of mRNA. As the sequencing coverage of methylome sequencing in a single cell was relatively low, single-cell whole genome bisulfte sequencing (scWGBS) was preferable to generate the methylome map in single-cell parallel sequencing in comparison to single-cell reduced representation bisulfte sequencing (scRRBS). To the best of our knowledge, this is the frst study to compare the two methods of single-cell parallel sequencing which ofers a basic idea for deciding between the two methods and a direction of single-cell parallel sequencing development. 1. Introduction Single-cell high throughout sequencing technology has been devel- oped at an amazing speed in recent ten years. The frst single-cell whole transcriptome sequencing was performed by Tang et al. in 2009 (Tang et al., 2009). Subsequently, single-cell whole genome sequencing and whole exome sequencing technologies were successively established in 2011 and 2012 (Hou et al., 2012; Navin et al., 2011). Besides genetics, epigenetics profles in single cells could also be generated through single-cell reduced representation bisulfte sequencing (scRRBS) or single cell whole genome bisulfte sequencing (scWGBS) (Nagano et al., 2013; Smallwood et al., 2014). Nowadays, such single cell sequencing technologies have been widely applied to explore cell heterogeneity, new cell types, cell diferentiation, embryonic development and so on. However, the above approaches only allow us to study DNA and RNA separately in the same cell. Since cell-to-cell variability has been de- monstrated in genomics, mRNA expression and also epigenetics and the complexity of gene expression regulation has been recognized, the conventional single cell sequencing methods could not actually uncover the causal relationship between epigenetic variations and mRNA tran- scription profles. Besides, in the study of several cell types, like female gametes, the collection of samples is limited. Thus, mulitomic assays can provide a better understanding of the same cell, particularly in the case of oocyte study. In 2016, single cell parallel sequencing technology was frstly re- ported to link transcriptome and genome simultaneously through ap- plying biotinylated oligo-dT primer coated magnetic beads to separate DNA and RNA in one cell (Angermueller et al., 2016). Similarly, in the same year, Youjin Hu, et al. reported another separation method. It gently isolated cytosolic RNA to resemble soma RNA, so DNA in the https://doi.org/10.1016/j.biocel.2018.12.003 Received 7 October 2018; Received in revised form 30 November 2018; Accepted 5 December 2018 ⁎ Corresponding author at: 622A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong Special Administrative Region, China. E-mail address: leetl@cuhk.edu.hk (T.-L. Lee). International Journal of Biochemistry and Cell Biology 107 (2019) 1–5 Available online 06 December 2018 1357-2725/ © 2018 Elsevier Ltd. All rights reserved. T