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Status |
Public on Dec 06, 2024 |
Title |
H3K27ac ChIP-seq: HS68 HCMV-infected Replicate 2 |
Sample type |
SRA |
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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.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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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 |
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Relations |
BioSample |
SAMN39709316 |
SRA |
SRX23483120 |