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New single-cell RNA-Seq method deciphers more secrets of human embryos

Peking University, Oct. 9, 2013: A research group from PKU has achieved a breakthrough: they devised a new single-cell RNA-Sequencing (RNA-Seq) method to successfully profile a comprehensive set of transcriptome landscapes of human pre-implantation embryos and human embryonic stem cells (hESC). The study has been published in the journal Nature Structural & Molecular Biology, September Issue.


The researchers unprecedentedly applied single-cell RNA-Seq analysis with global gene expression analysis to 124 individual cells at different passages and discovered 2,733 novel long noncoding RNAs (lncRNAs). They analyzed the gene expression characteristics of human late blastocysts and for the first time in science history separated them into three lineages -- trophectoderm (TE), epiblast (EPI) and primitive endoderm (PE). They have also historically documented the dynamics of global gene expression during the process of hESC derivation and found significant difference in transcriptomes between that EPI cells and primary hESC outgrowth, which addressed the long-standing question whether gene expression signatures of the two are the same.




A transcriptome is all the RNA that a cell can transcript. Deciphering the temporal and spatial patterns of gene expression in human embryos is a crucial step toward understanding the molecular mechanism that regulates human’s early embryonic development, which is still largely unknown due to technical difficulties and scarcity of human samples. The results pave the way for dissecting the molecular regulation and provide insight into pluripotency and the molecular identity of hESCs.


During the study, their new method was tested against an alternative commercialized single-cell RNA-Seq method, SMART-Seq and turned out to be able to recover more expressed genes, have better coverage for 5’ ends of the cDNAs and showing better technical reproducibility.




The research project was carried out through a joint effort of Professor Qiao Jie’s team from PKU Third Hospital with the Researcher Tang Fuchou and Li Ruiqiang’s team from Biodynamics Optical Imaging Center, School of Life Sciences. It was supported by National Basic Research Program of China (973 Program) and National Natural Science Foundation of China.


Edited by: Chen Long

Source: Biodynamic Optical Imaging Center