GEO DataSets

(Submitter supplied) 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.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

25 Samples

Download data: BW

(Submitter supplied) Using PRO-Seq, which profiles nascent transcripts, and a recently developed DFF-ChIP approach that informs on local chromatin environment, we show that IE2 controls viral gene transcription in three distinct capacities during late HCMV infection and reveal mechanisms involving direct binding of IE2 to viral DNA. IE2 represses a subset of viral promoters by binding within the target core promoter region, blocking the assembly preinitiation complexes (PICs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

38 Samples

Download data: BW

(Submitter supplied) Herpesvirus late promoters activate gene expression after viral DNA synthesis has begun. Alphaherpesviruses utilize a viral immediate-early protein to do this, whereas beta- and gammaherpesviruses primarily use a 6-member set of viral late-acting transcription factors (LTF) that are drawn to a TATT sequence in the late promoter. The betaherpesvirus, human cytomegalovirus (HCMV), produces three immediate-early 2 protein isoforms, IE2-86, IE2-60, IE2-40, in late infection, but whether they activate late viral promoters is unknown. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

22 Samples

Download data: BED, BW

(Submitter supplied) We report ChIP-seq analsyis of human fibroblasts infected with HCMV strains AD169 and TB40E. ChIP was performed at 20 hpi for IE2 and 3 dpi for IE2 and UL84.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: WIG

(Submitter supplied) We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

13 Samples

Download data: BB, BW

(Submitter supplied) Herpesviruses have a group of genes earmarked for expression late in the infection. Beta- and gammaherpesviruses utilize a six-member set of viral late transcription factors to selectively activate these genes by binding to a DNA sequence signature in gene promoters. We made an unexpected discovery that differences in sequence signature configures the late gene expression program for human cytomegalovirus, a beta-herpesvirus of global public health importance. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20795 GPL20301

24 Samples

Download data: BW

(Submitter supplied) Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. more...

Organism:

Human betaherpesvirus 5

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platform:

GPL17446

33 Samples

Download data: GFF, PAIR

(Submitter supplied) Purpose: To identify interactions of the viral DNA-binding protein, UL34, with the viral genome during lytic-phase replication. Methods: Human fibroblasts were infected with human cytomegalovirus expressing Myc-tagged UL34 in biological duplicate. At 48 hours post infection, ChIP was performed with anti-Myc tag antibody (Cell Signaling) and the resulting DNA fragments were sequenced on Illumina MiSeq. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15520

4 Samples

Download data: TXT

(Submitter supplied) We describe the influence of the RNA binding protein ZAP (ZC3HAV1) on the CMV gene expression cascade

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL18573 GPL24676

54 Samples

Download data: BW, NARROWPEAK, TSV

(Submitter supplied) These data files consist of Illumina next seq 500 sequencing data from precision nuclear run-on and global nuclear run-on experiments conducted with human epithelial Hep2 cells that have been infected with human herpes simplex virus-1 (F) strain mutants. The results of these studies suggest that ICP22 is necessary for reducing Pol II processivity on the viral genome which results in its maintenance on the viral genome over the course of infection. more...

Organism:

Drosophila melanogaster; Homo sapiens; Human alphaherpesvirus 1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29914

32 Samples

Download data: BW

(Submitter supplied) The abundance of HSV mRNAs was determines over 16h of infection in wt (KOS) and n199 (ICP22 mutant) infected cells. ICP22 is an immediate early gene of HSV that affects gene expression

Organism:

Human alphaherpesvirus 1; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23890

12 Samples

Download data: XLSX

(Submitter supplied) The goal of this study was to understand changes that occur in RNA polymerase II occupancy upon heat shock using ChIP-seq in mouse cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002

4 Samples

Download data: BEDGRAPH

(Submitter supplied) The goal of this study was to determine how RNA poymerase II (Pol II) occupancy changed in response to herpes simplex virus-1 (HSV-1) infection using ChIP-seq of Pol II. ChIP assays were performed 4 hours after cells were infected (or mock infected) with HSV-1. Because host cell Pol II transcribes the HSV-1 genome, the ChIP-seq data also reveal polymerase occupancy on the viral genome.

Organism:

Mus musculus; Human alphaherpesvirus 1 strain KOS

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19845 GPL13112

3 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL29977 GPL24676

25 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: to investigate the role of the HCMV immediate early genes in controlling the HCMV and cellular transcriptomes

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29977

4 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: to investigate expression of HCMV and cellular RNAs at early times post-infection in a lytic model

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29977

2 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: to investigate the human transcriptome in MRC5 fibroblasts

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: to investigate the role of the HCMV immediate early proteins in controlling the HCMV and cellular epigneomes during lytic infectioin

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29977

16 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: to investigate occupancy of Pol II and H3K27Ac on the HCMV and cellular genomes at early times post-infection in a lytic model

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29977

8 Samples

Download data: BIGWIG