Accession	GSE185246
Status	2023/6/20
Title	The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ChIPmentation)
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	To look at the deposition of the histone marks in the downstream regions of DoTT genes, HFFF cells were either mock, WT HSV-1 (strain F and 17) or ΔICP22 virus infected. Throught the course of infection (for the marked samples), cells were treated with 350 ug/ml PAA. Samples were processed according to the original ChIPmentation protocol (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015) with few changes as explained in the Materials and Methods section.
Samples	GSM ID Sample info Characteristics Description GSM5608709 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H1, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608710 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H1, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608711 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608712 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608713 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H4, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608714 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H4, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608715 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K27me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608716 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K27me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608717 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K36me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608718 HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K36me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608719 HFFF cells mock 8h infected, PAA treated, histone H1, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608720 HFFF cells mock 8h infected, PAA treated, histone H1, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608721 HFFF cells mock 8h infected, PAA treated, histone H3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608722 HFFF cells mock 8h infected, PAA treated, histone H3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608723 HFFF cells mock 8h infected, PAA treated, histone H4, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608724 HFFF cells mock 8h infected, PAA treated, histone H4, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608725 HFFF cells mock 8h infected, PAA treated, histone H3K27me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608726 HFFF cells mock 8h infected, PAA treated, histone H3K27me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608727 HFFF cells mock 8h infected, PAA treated, histone H3K36me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608728 HFFF cells mock 8h infected, PAA treated, histone H3K36me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608729 HFFF cells infected with HSV-1 WT (F), 8hpi, PAA treated, histone H1, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain F DNA isolated with Zymo DNA Clean & Concentrator GSM5608730 HFFF cells infected with HSV-1 WT (F), 8hpi, PAA treated, histone H1, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: HSV-1 WT, strain F DNA isolated with Zymo DNA Clean & Concentrator GSM5608731 HFFF cells infected with deltaICP22 (F), 8hpi, PAA treated, histone H1, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: deltaICP22, strain F DNA isolated with Zymo DNA Clean & Concentrator GSM5608732 HFFF cells infected with deltaICP22 (F), 8hpi, PAA treated, histone H1, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: deltaICP22, strain F DNA isolated with Zymo DNA Clean & Concentrator GSM5608733 HFFF cells mock infected, PAA treated, histone H1, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608734 HFFF cells mock infected, PAA treated, histone H1, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: PAA (350 microg/ml);infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608735 HFFF cells mock infected, histone H3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608736 HFFF cells mock infected, histone H3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608737 HFFF cells infected with HSV-1 WT (17), histone H3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608738 HFFF cells infected with HSV-1 WT (17), histone H3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608739 HFFF cells mock infected, histone H3K27me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608740 HFFF cells mock infected, histone H3K27me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608741 HFFF cells infected with HSV-1 WT (17), histone H3K27me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608742 HFFF cells infected with HSV-1 WT (17), histone H3K27me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608743 HFFF cells mock infected, histone H3K36me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608744 HFFF cells mock infected, histone H3K36me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608745 HFFF cells mock infected, histone H3K36me3, replicate 3 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: mock DNA isolated with Zymo DNA Clean & Concentrator GSM5608746 HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 1 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608747 HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 2 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator GSM5608748 HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 3 cell type: Human fetal foreskin fibroblasts;treatment: no treatment;infection: HSV-1 WT, strain 17 DNA isolated with Zymo DNA Clean & Concentrator
Platform	GPL18573  GPL28038  : Illumina NextSeq 500 (Homo sapiens);DNBSEQ-G400 (Homo sapiens)
Literature	37524699