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Sample GSM8056990 Query DataSets for GSM8056990
Status Public on Dec 06, 2024
Title H3K27ac ChIP-seq: HS68 HCMV-infected Replicate 2
Sample type SRA
 
Source name HS68
Organism Homo sapiens
Characteristics cell line: HS68
cell type: Foreskin fibroblast
infection: TB40/E HCMV
chip antibody: Abcam ab4729, lot GR3357415-1
Treatment protocol HS68 cells were infected with the TB40/E clinical isolate of HCMV at a multiplicity of infection (MOI) of 5. Cells were harvested 48 hours post infection.
Growth protocol HS68 cells were maintained in DMEM supplemented with 10% HyClone FetalClone III serum (FC-III) and antiobiotics in a humidified incubator with 5% CO2 at 37 C.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared using the NEBNext Ultra II kit (NEB #E7645S) as per the instructions provided by the manufacturer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing We performed quality control of raw sequencing reads using the ChIP-seq transcription factor Pipeline v2.2.0 from the ENCODE Project (https://www.encodeproject.org/pipelines/).
ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2. Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using the default parameters of MACS2.
The ENCODE blacklist region was removed upon establishing the final peak set.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each condition and used for downstream analyses.
DiffBind was used to find differential and non-differential ("shared") peaks using the conservative overlap peaksets. Peaks were considered significantly differential if the FDR was less than 0.01 and the fold change was at least 2-fold.
Assembly: hg19
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10
Supplementary files format and content: Peaks identified as either differential or shared by DiffBind. Files are in tsv format and contain the standard DiffBind output.
 
Submission date Jan 31, 2024
Last update date Dec 06, 2024
Contact name Matthew Weirauch
E-mail(s) Matthew.Weirauch@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Center for Autoimmune Genomics and Etiology (CAGE)
Street address 3333 Burnet Avenue
City Cincinnati
State/province Ohio
ZIP/Postal code 45229-3026
Country USA
 
Platform ID GPL24676
Series (2)
GSE254736 Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [ChIP-seq]
GSE254741 Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity
Relations
BioSample SAMN39709316
SRA SRX23483120

Supplementary file Size Download File type/resource
GSM8056990_H3K27ac_ChIP_HS68_HCMV_rep2.hg19.bw 203.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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