Journal
Genome biology
Publication Date
9-28-2020
Volume
21
Issue
1
First Page
255
Document Type
Open Access Publication
DOI
10.1186/s13059-020-02164-3
Rights and Permissions
Miao, B., Fu, S., Lyu, C. et al. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biol 21, 255 (2020). https://doi.org/10.1186/s13059-020-02164-3 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.
Recommended Citation
Miao, Benpeng; Fu, Shuhua; Lyu, Cheng; Gontarz, Paul; Wang, Ting; and Zhang, Bo, "Tissue-specific usage of transposable element-derived promoters in mouse development." Genome biology. 21, 1. 255 (2020).
https://digitalcommons.wustl.edu/oa_4/469
The epigenomic data of five tissues at embryonic day 14.5 and postnatal day 0 development stages from the ENCODE.
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The accessible TEs identified in the five tissues.
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The spatial correlation between open chromatin regions and transposable elements (TEs) in five tissues.
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Tables S1-S7
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Figures S1-S10
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The spatial correlation between open chromatin regions and transposable elements (TEs) in five tissues.
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Table S1. The number of accessible TEs located in the gene’s promoter and contributed to the TSS of genes. Table S2. The annotation of accessible TE that derived TSS of genes in five tissue. Table S3. Examples of accessible TEs that derived TSS.
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Table S1. The dynamic changes of accessible TEs between two development stages of five tissues. Table S2. The number of stage-specific accessible TEs located in the gene’s promoter regions. Table S3-S7. The enriched TF binding motifs of stage-specific accessible TEs in intestine, liver, lung, stomach, and kidney. Table S8. Expression of TF genes at two development stages of five tissues.
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Table S1. The evolutionary conservation of open chromatin regions with TEs or without TEs across five mouse tissues by comparing with the human and rat genome. Table S2. Conservation of accessible TEs that contained the TSSs of genes in mouse, rat, and human. Table S3. The ortholog of accessible TE-derived TSS genes in mouse, rat, and human. Table S4. The ortholog of accessible TE-derived lincRNAs in three species.
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The percentage of identity, coverage, and gaps for the exon’s alignment between Timd2 and Havcr1 genes.
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Table S1. The number of genes that their transcripts used 5′ end TE-derived TSS and non-TE derived TSS. Table S2. The usage of TE-derived TSS in the transcripts of genes overlapped CAGE peaks.
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Review history.
