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. 2017 Jun 16;7:3729. doi: 10.1038/s41598-017-03829-z

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Comparisons of RNA-Seq gene expression levels between the X chromosome and autosomes in mouse early embryogenesis. (A) Schematic illustration of the process of inactivation in mouse early embryogenesis: The initiation of iXCI begins at early preimplantation in embryos and Xp-Xist is expressed around the four-cell stage. Next, the active paternal X chromosome becomes gradually inactive from the four-cell stage to early blastocyte stage to form a process from X reactivation to X inactivation. (B) X: A ratios of median expressions according to all reads for each sex and embryonic day. There were no differences between each types of embryonic cells and between males and females. (P > 0.05, by Student’s t-test). (C) X: AA ratios of median expressions according to SNP-containing reads for each sex and embryonic day. There were no differences between each types of embryonic cells and between males and females. (P > 0.05, by Student’s t-test). (D) Boxplots showing the distribution of cellular X chromosome FPKM sums for each sex and embryonic day. There were no differences between each types of embryonic cells and between males and females. (P > 0.05, by Student’s t-test). (E) Comparisons of X: AA ratios of median expressions between paternal X chromosome and maternal X chromosome from female 4-cell stage (N = 11), 16-cell stage (N = 21) and early blastocyst stage (N = 15) in female embryo. (F) Comparisons of X: AA ratios of median expressions between paternal X chromosome and maternal X chromosome from male 4-cell stage (N = 3), 16-cell stage (N = 27) and early blastocyst stage (N = 28) in male embryo. N represents the number of single cell RNA-seq data with this stage in the parentheses after early embryogenesis. The percentiles in all boxplots are 0.05, 0.25, 0.5, 0.75 and 0.95.