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

Abstract

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.

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Figure 1: Morphology and marker gene expression of human early embryos and hESCs.
Figure 2: Global expression patterns of known RefSeq genes during the seven consecutive stages of human preimplantation development.
Figure 3: Dynamic patterns of alternative splicing during the seven consecutive stages of human preimplantation development and derivation of hESCs.
Figure 4: Expression patterns of known long noncoding RNA (lncRNA) genes during human preimplantation development and derivation of hESCs.
Figure 5: Expression patterns of novel lncRNAs during human preimplantation development.
Figure 6: The EPI, PE and TE lineage segregation in the blastocysts.

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Gene Expression Omnibus

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Acknowledgements

F.T. was supported by grants from the National Basic Research Program of China (2012CB966704 and 2011CB966303) and National Natural Science Foundation of China (31271543). J.Q. was supported by grants from the National Basic Research Program of China (2011CB944500) and the National Natural Science Funds for Distinguished Young Scholar (30825038). L.Y. was supported by a grant from the National Science Foundation of China (81000275). We would like to thank S. Gao, Y. Zhang, P. Xu, S. Lin, X. Ren, Q. Zhang, Y. Jiang, M. Fan, J. Li, X. Zhuang, W. Song and Y. Chen for their great help.

Author information

Authors and Affiliations

Authors

Contributions

J.Q. and F.T. conceived and designed the project, and R.L. was in charge of the bioinformatic analysis. L. Yan, H.G., L. Yang, X.W. and L.W. conducted the majority of the experiments. M.Y. and J.W. did all of the data analysis. R.L., P.L., Y.L., X.Z., J.Y., J.H. and M.L. contributed to oocyte collection, sperm treatment and embryo culture in vitro. L. Yan, M.Y., K.L., R.L., J.Q. and F.T. prepared the manuscript. All authors contributed to the revision of the manuscript.

Corresponding authors

Correspondence to Ruiqiang Li, Jie Qiao or Fuchou Tang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Note (PDF 9845 kb)

Supplementary Table 1

Expression (RPKM) of known RefSeq genes in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 20445 kb)

Supplementary Table 2

Expression (RPKM) of known RefSeq transcripts in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 28202 kb)

Supplementary Table 3

GO enrichment analysis for EPI-specific genes compared to all the other cells after the 8-cell stage (including 8-cell–stage embryos). (XLSX 62 kb)

Supplementary Table 4

Number of exon-exon junction reads that are unique to transcript isoforms of known RefSeq genes in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 4632 kb)

Supplementary Table 5

Expression (counts) of known lncRNA genes in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 11064 kb)

Supplementary Table 6

Expression (counts) of novel transcripts in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 3520 kb)

Supplementary Table 7

Expression (RPKM) of the differentially expressed genes among the epiblast (EPI), primitive endoderm (PE) and trophectoderm (TE) lineages of late blastocysts. (XLSX 6580 kb)

Supplementary Table 8

Expression (RPKM) of the differentially expressed genes between the epiblast (EPI) cells of late blastocysts and passage #0 hESCs. (XLSX 156 kb)

Supplementary Table 9

The rRNA contamination in the single cell RNA-Seq data for 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 51 kb)

Supplementary Table 10

Summary of the sequencing exercise, quality control (Q20 and Q30 percentage of the sequencing reads) and mapped rates of RNA-Seq data to RefSeq, Ensemble, known lncRNAs, and genome of 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 71 kb)

Supplementary Table 11

The distribution of all mapped reads in different features (exon, intron and intergenic) of the human genome in 124 single cells from mature oocytes, preimplantation embryos and embryonic stem cells. (XLSX 54 kb)

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Yan, L., Yang, M., Guo, H. et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 20, 1131–1139 (2013). https://doi.org/10.1038/nsmb.2660

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