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. 2018 Mar 29;9:1281. doi: 10.1038/s41467-018-03668-0

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© The Author(s) 2018

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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Fig. 1 — Identification of NO-responsive transcripts and Zeb1-associated genomic regions. a Heatmap showing the 50 most differentially regulated genes in mESC cultured for 24 h in GS, DM, or NO identified by total RNA sequencing analysis (n = 3 each group). Red and blue represent over- and under-expressed genes, respectively. b Venn diagrams depicting the distribution of upregulated (upper panel) and downregulated (lower panel) unique or common transcripts among GS, DM, or NO conditions. c Left panel: MA plot of differentially regulated genes expressed in mESC cultured for 24 h in NO compared to GS condition. Red dots show genes with a p adjusted value <0.05. Right panels: Gene ontology analysis of NO-differentially regulated transcripts between mESC cultured in GS and NO. Upregulated genes depicted in the upper panel, red bar graph; downregulated genes in the lower panel, blue bar graph. d Distribution of chromatin–associated Zeb1 regions over mouse chromosomes. Black bars: percentage of all chromatin/Zeb1-associated regions; gray bars: background derived from input samples (n = 3). e The pie chart illustrates the distribution of chromatin-associated Zeb1 regions (Zeb1-ChIP) over specific genomic features depicted as follows: (i) promoters encompassing 3000 bp upstream of the transcription start site (TSS) (blue sector); (ii) downstream regions encompassing 3000 bp from transcription end site (TES) (red sector); 5′ UTRs (green sector) and 3′ UTRs (purple sector) as well as coding exons (turquoise sector) and introns (orange sectors) relative to the gene bodies; iii) distal intergenic regions (light blue sectors). Input and Zeb1-ChIP represented in the left and right pie chart respectively. f Gene body profile depicting Zeb1-ChIP regions distribution in association with TSS or TES produced by ngsplot