Virus Dataset Detail

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Dataset Information
Accession GSE280380
Status 2025/1/1
Title DNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing;Genome binding/occupancy profiling by high throughput sequencing
Summary We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4).
Samples
GSM ID Sample info Characteristics Description
GSM8724535 HFF cells, H3K14ac, HSV1, 6hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K14ac_HSV1_6hpi_rep1
GSM8724536 HFF cells, H3K14ac, HSV1, 6hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K14ac_HSV1_6hpi_rep2
GSM8724537 HFF cells, H3K14ac, HSV1, 14hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K14ac_HSV1_14hpi_rep1
GSM8724538 HFF cells, H3K14ac, HSV1, 14hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K14ac_HSV1_14hpi_rep2
GSM8595840 HFF cells, mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:mock -
GSM8595841 HFF cells, mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:mock -
GSM8595842 HFF cells, HCMV(BAC2), 12h, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595843 HFF cells, HCMV(BAC2), 12h, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595844 HFF cells, HCMV(BAC2), 36h, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595845 HFF cells, HCMV(BAC2), 36h, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595846 HFF cells, HCMV(BAC2), 72h, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595847 HFF cells, HCMV(BAC2), 72h, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HCMV(BAC2) -
GSM8595848 SLK endothelial cells, mock, rep1 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:mock -
GSM8595849 SLK endothelial cells, mock, rep2 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:mock -
GSM8595850 SLK endothelial cells, KSHV, 24h, rep1 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595851 SLK endothelial cells, KSHV, 24h,, rep2 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595852 SLK endothelial cells, KSHV, 48h, rep1 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595853 SLK endothelial cells, KSHV, 48h, rep2 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595854 SLK endothelial cells, KSHV, 72h, rep1 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595855 SLK endothelial cells, KSHV, 72h, rep2 tissue:cell line; cell line:SLK endothelial cells; cell type:SLK endothelial cells; genotype:KSHV_inducible; treatment:dox -
GSM8595856 HFF cells, DUX4, mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:mock -
GSM8595860 HFF cells, DUX4, 24h, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:dox -
GSM8595857 HFF cells, DUX4, mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:mock -
GSM8595858 HFF cells, DUX4, 8h, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:dox -
GSM8595861 HFF cells, DUX4, 24h, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:dox -
GSM8595859 HFF cells, DUX4, 8h, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:DUX4_inducible; treatment:dox -
GSM8595862 293T cells, DUX4, mock, rep1 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:mock -
GSM8595863 293T cells, DUX4, mock, rep2 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:mock -
GSM8595864 293T cells, DUX4, 8h, rep1 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:dox -
GSM8595865 293T cells, DUX4, 8h, rep2 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:dox -
GSM8595866 293T cells, DUX4, 12h, rep1 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:dox -
GSM8595867 293T cells, DUX4, 12h, rep2 tissue:cell line; cell line:293T; cell type:HEK 293T cells; genotype:DUX4_inducible; treatment:dox -
GSM8595868 HFF cells, KAP1, mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:mock -
GSM8595869 HFF cells, KAP1, mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:mock -
GSM8595870 HFF cells, KAP1, HSV1, 6hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8595871 HFF cells, KAP1, HSV1, 6hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8595872 HFF cells, KAP1, HSV1, 14hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8595873 HFF cells, KAP1, HSV1, 14hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8595874 HFF cells, IgG, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8595875 HFF cells, IgG, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 -
GSM8724521 HFF cells, SETDB1, Mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: SETDB1_Mock_rep1
GSM8724522 HFF cells, SETDB1, Mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: SETDB1_Mock_rep2
GSM8724523 HFF cells, SETDB1, HSV1, 6hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: SETDB1_HSV1_6hpi_rep1
GSM8724524 HFF cells, SETDB1, HSV1, 6hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: SETDB1_HSV1_6hpi_rep2
GSM8724525 HFF cells, SETDB1, HSV1, 14hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: SETDB1_HSV1_14hpi_rep1
GSM8724526 HFF cells, SETDB1, HSV1, 14hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: SETDB1_HSV1_14hpi_rep2
GSM8724527 HFF cells, H3K9me3, Mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: H3K9me3_Mock_rep1
GSM8724528 HFF cells, H3K9me3, Mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: H3K9me3_Mock_rep2
GSM8724529 HFF cells, H3K9me3, HSV1, 6hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K9me3_HSV1_6hpi_rep1
GSM8724530 HFF cells, H3K9me3, HSV1, 6hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K9me3_HSV1_6hpi_rep2
GSM8724531 HFF cells, H3K9me3, HSV1, 14hpi, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K9me3_HSV1_14hpi_rep1
GSM8724532 HFF cells, H3K9me3, HSV1, 14hpi, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:HSV1 Library name: H3K9me3_HSV1_14hpi_rep2
GSM8724533 HFF cells, H3K14ac, Mock, rep1 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: H3K14ac_Mock_rep1
GSM8724534 HFF cells, H3K14ac, Mock, rep2 tissue:cell line; cell line:HFF; cell type:HFF cells; genotype:WT; treatment:Mock Library name: H3K14ac_Mock_rep2
Platform GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
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* p<0.05 ** p<0.01