Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

• Published in: Nature structural & molecular biology Vol. 20; no. 9; pp. 1131 - 1139
• Main Authors: Yan, Liying, Yang, Mingyu, Guo, Hongshan, Yang, Lu, Wu, Jun, Li, Rong, Liu, Ping, Lian, Ying, Zheng, Xiaoying, Yan, Jie, Huang, Jin, Li, Ming, Wu, Xinglong, Wen, Lu, Lao, Kaiqin, Li, Ruiqiang, Qiao, Jie, Tang, Fuchou
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2013; Nature Publishing Group
• Subjects: 631/136/2086; 631/136/532/2117; 631/1647/514/1949; 631/337/384/2568; Alternative Splicing; Analysis; Biochemistry; Biological Microscopy; Blastocyst - cytology; Blastocyst - metabolism; Blastomeres - cytology; Blastomeres - metabolism; Developmental stages; DNA microarrays; Embryo Culture Techniques; Embryology; Embryonic growth stage; Embryonic stem cells; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Embryos; Female; Gene expression; Gene Expression Profiling; Genetic aspects; Germ Layers - cytology; Germ Layers - metabolism; Humans; Life Sciences; Membrane Biology; Methods; Molecular biology; Oocytes - metabolism; Physiological aspects; Pluripotent Stem Cells - cytology; Pluripotent Stem Cells - metabolism; Protein Structure; resource; Ribonucleic acid; RNA; RNA sequencing; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Sequence Analysis, RNA; Single-Cell Analysis; Stem cells; Transcriptome; China
• ISSN: 1545-9993; 1545-9985; 1545-9985
• DOI: 10.1038/nsmb.2660

Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Single-cell RNA sequencing (RNA-Seq) analysis of 124 individual cells from human preimplantation embryos and embryonic stem cells (hESCs) now provides a comprehensive framework of the transcriptome landscapes of human early embryos and hESCs. Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Here we apply single-cell RNA sequencing (RNA-Seq) analysis to 124 individual cells from human preimplantation embryos and human embryonic stem cells (hESCs) at different passages. The number of maternally expressed genes detected in our data set is 22,687, including 8,701 long noncoding RNAs (lncRNAs), which represents a significant increase from 9,735 maternal genes detected previously by cDNA microarray. We discovered 2,733 novel lncRNAs, many of which are expressed in specific developmental stages. To address the long-standing question whether gene expression signatures of human epiblast (EPI) and in vitro hESCs are the same, we found that EPI cells and primary hESC outgrowth have dramatically different transcriptomes, with 1,498 genes showing differential expression between them. This work provides a comprehensive framework of the transcriptome landscapes of human early embryos and hESCs.