|
| Status |
Public on May 11, 2022 |
| Title |
IE2-GFP-Standard ChIP Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Human Foreskin Fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Foreskin Fibroblast
treatment: Untreated
infection: HCMV TB40/E IE2-GFP 48 h
chip antibody: GFP-Trap agarose (Chromotek gta-10)
|
| Treatment protocol |
HFF were infected at an MOI of 3 with the indicated virus for the indicated times. DMSO vehicle control or dTAG treatments were carried out for 6 or 12 h as previously described.
|
| Growth protocol |
HFF cells were maintained in DMEM (Gibco 11965-092) supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNA-Seq, cells were directly lysed in Trizol, and extracted and DNase treated prior to quality control analysis as described in the text. For standard ChIP-Seq, cells were fixed in 1% formaldehyde, harvested, and frozen as described in the text. Chromatin was sheared and ChIP was performed as detailed in the methods. For DFF-ChIP, native isolated nuclei or crosslinked cells were harvested as described in the methods, and chromatin was digested with DFF for 1 hour at 37° C. Soluble chromatin was extracted and ChIP was carried out as described in the methods.
Details of library construction for each type of assay are provided in the methods.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2 (ChIP-Seq) or hisat2 (RNA-Seq)
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38 (human), KF297339.1 (HCMV TB40/E), FJ616285.1 (HCMV Towne)
Supplementary_files_format_and_content: bigwig files containing pileup of normalized RNA-Seq data and ChIP data
|
| |
|
| Submission date |
Jan 04, 2022 |
| Last update date |
May 11, 2022 |
| Contact name |
David H Price |
| E-mail(s) |
david-price@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Department of Biochemistry and Molecular Biology
|
| Street address |
431 Newton Road
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE193026 |
Human cytomegalovirus IE2 both activates and represses initiation and modulates elongation in a context-dependent manner |
|
| Relations |
| BioSample |
SAMN24611862 |
| SRA |
SRX13601008 |
