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. 2023 Jul 25;14:1202163. doi: 10.3389/fimmu.2023.1202163

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Copyright © 2023 Farley, Chengrui, Palmer, Liu, Kousa, Rouse, Major, Sweetman, Morys, Corsinotti, Nichols, Ure, McLay, Boulter, Chapman, Tomlinson and Blackburn

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Identification of candidate regulatory networks in E10.5 and E12.5 TEC. (A) Heat map shows SCENIC scores of transcription factors relevant to each cluster. (B) Network constructed with regulons and their control targets. Arrows indicate control relationships. Red boxes show genes upregulated in Cluster 7 but not in Cluster 5 or 6. Black boxes show genes expressed in all E12.5 TEC clusters. Grey boxes show genes upregulated in E12.5 Clusters 5 and 6 compared to Cluster 7. Blue arrows highlight Sox9 and Foxn1 nodes. (C) Images show wholemount immunostaining of thick transverse sections of the pharyngeal region containing the thymic primordia from Foxn1^GFP embryos at the ages and for the markers shown. Scale bars are as indicated. Note that in the E12.5 and E13.5 images the cells immediately outside the epithelial region that stain with all markers are autofluorescent.