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. 2024 Jun 27;22:143. doi: 10.1186/s12915-024-01939-5

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Mouse AGM scATAC-seq analysis and accessible TE identification. A Cell types recovered from mouse scATAC-seq data. B UMAP of EHT marker gene activities. Cdh5 marks endothelial cells, Lyve1 marks VECs, Hey1 marks AECs, Gja5 marks pre-HECs and partial AECs, Runx1 marks HECs/HSCs, and Ptprc marks HSCs. C Differential accessible analysis of TEs in pre-HECs versus endothelial clusters (VECs and AECs). D Cell type-specific open TEs identified in mouse EHT. E TE composition and potential cis-regulatory functions of cell type-specific open TEs. F Overlaps of all cell type-specific accessible peaks with different TE superfamilies. G Tracks of normalized signals in each cell type, genes, TEs, ELSs, peaks, and CCANs. Two potential enhancers derived by TEs and the promoter of Gja5 transcripts are highlighted with light grey bars