Accession	GSE185618
Status	2022/2/17
Title	Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	To investigate the chromatin structure surrounding human RNA polymerase II (Pol II) transcription on host and viral genomes, chromatin immunoprecipitation (ChIP) was performed following digestion of HCMV infected primary human foreskin fibroblasts (HFFs) with DNA Fragmentation Factor (DFF). DFF is a human endonuclease responsible for cleaving between nucleosomes during apoptosis. We found that utilizing DFF as the front end for ChIP-Seq in place of sonication or Micrococcal nuclease (MNase) offered new insights into the connections between active transcription and the local chromatin on the host and that these connections were completely absent on the HCMV genome.
Samples	GSM ID Sample info Characteristics Description GSM5620722 HFF cells, UL87 DFF ChIP-Seq (Sample 15) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:UL87; treatment:untreated; condition:Low Salt; exp:4 - GSM5620723 HFF cells, H3K4me3 DFF ChIP-Seq (Sample 16) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:4 - GSM5620724 HFF cells, Pol II DFF ChIP-Seq Rep1 (Sample 17) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:Pol II; treatment:untreated; condition:Low Salt; exp:5 - GSM5620725 HFF cells, Pol II DFF ChIP-Seq Rep2 (Sample 18) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:Pol II; treatment:untreated; condition:Low Salt; exp:5 - GSM5620726 HFF cells, Ser5P DFF ChIP-Seq Rep1 (Sample 19) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:Ser5P; treatment:untreated; condition:Low Salt; exp:5 - GSM5620727 HFF cells, Ser5P DFF ChIP-Seq Rep2 (Sample 20) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:Ser5P; treatment:untreated; condition:Low Salt; exp:5 - GSM5620728 HFF cells, TBP DFF ChIP-Seq Rep1 (Sample 21) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:TBP; treatment:untreated; condition:Low Salt; exp:5 - GSM5620729 HFF cells, TBP DFF ChIP-Seq Rep2 (Sample 22) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:TBP; treatment:untreated; condition:Low Salt; exp:5 - GSM5620730 HFF cells, H3K4me3 DFF ChIP-Seq Rep 1 (Sample 23) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:5 - GSM5620731 HFF cells, H3K4me3 DFF ChIP-Seq Rep 2 (Sample 24) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:5 - GSM5620732 HFF cells, UL87 DFF ChIP-Seq Rep1 (Sample 25) cell type:HFF; infection (duration and strain):48 hrs Towne BAC; chip antibody:UL87; treatment:untreated; condition:Low Salt; exp:5 - GSM5620708 MRC5 cells, Pol II DFF ChIP-Seq (Sample 1) cell line:MRC5; infection (duration and strain):uninfected; chip antibody:GFP; treatment:Flavo; condition:Low Salt; exp:1 - GSM5620709 HeLa cells, H3K4me3 DFF ChIP-Seq (Sample 2) cell line:HeLa; infection (duration and strain):uninfected; chip antibody:H3K4me3; treatment:Flavo; condition:Low Salt; exp:1 - GSM5620710 MRC5 cells, H3K4me3 DFF ChIP-Seq (Sample 3) cell line:MRC5; infection (duration and strain):uninfected; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:2 - GSM5620711 MRC5 cells, H3K4me3 DFF ChIP-Seq (Sample 4) cell line:MRC5; infection (duration and strain):uninfected; chip antibody:H3K4me3; treatment:Flavo; condition:Low Salt; exp:2 - GSM5620712 MRC5 cells, Pol II DFF ChIP-Seq (Sample 5) cell line:MRC5; infection (duration and strain):uninfected; chip antibody:GFP; treatment:untreated; condition:High Salt; exp:2 - GSM5620713 MRC5 cells, Pol II DFF ChIP-Seq (Sample 6) cell line:MRC5; infection (duration and strain):uninfected; chip antibody:GFP; treatment:Flavo; condition:High Salt; exp:2 - GSM5620714 HFF cells, H3K4me3 DFF ChIP-Seq (Sample 7) cell type:HFF; infection (duration and strain):uninfected; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:3 - GSM5620715 HFF cells, Pol II DFF ChIP-Seq (Sample 8) cell type:HFF; infection (duration and strain):uninfected; chip antibody:Pol II; treatment:untreated; condition:Low Salt; exp:3 - GSM5620716 HFF cells, H3K4me3 DFF ChIP-Seq (Sample 9) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:H3K4me3; treatment:untreated; condition:Low Salt; exp:3 - GSM5620717 HFF cells, Pol II DFF ChIP-Seq (Sample 10) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:Pol II; treatment:untreated; condition:Low Salt; exp:3 - GSM5620718 HFF cells, Pol II DFF ChIP-Seq (Sample 11) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:Pol II; treatment:untreated; condition:Low Salt; exp:4 - GSM5620719 HFF cells, Pol II DFF ChIP-Seq (Sample 12) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:Pol II; treatment:Triptolide; condition:Low Salt; exp:4 - GSM5620720 HFF cells, TBP DFF ChIP-Seq (Sample 13) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:TBP; treatment:untreated; condition:Low Salt; exp:4 - GSM5620721 HFF cells, Ser5P DFF ChIP-Seq (Sample 14) cell type:HFF; infection (duration and strain):48 hrs Towne TB40e; chip antibody:Ser5P; treatment:untreated; condition:Low Salt; exp:4 -
Platform	GPL20301  GPL24676  : Illumina HiSeq 4000 (Homo sapiens);Illumina NovaSeq 6000 (Homo sapiens)
Literature	35579393
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