|
| Status |
Public on Feb 17, 2022 |
| Title |
HFF cells, H3K4me3 DFF ChIP-Seq (Sample 9) |
| Sample type |
SRA |
| |
|
| Source name |
Primary human foreskin fibroblast (HFF)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HFF
infection (duration and strain): 48 hrs Towne TB40e
chip antibody: H3K4me3
treatment: untreated
condition: Low Salt
exp: 3
|
| Treatment protocol |
Treatment Protocol: 1 hour prior to harvest, when cell were at 80-90% confluence, 5 ml of media was removed and either 25 µl of DMSO or 1 mM flavopiridol in DMSO was added before the mixture was returned to the flask (final concentrations 0.1% DMSO or 1 µM flavopiridol and 0.1% DMSO). Nuclei isolated from these cells were digested with ~15 µg of DFF per T150. (~25 µg for excess digestion experiments)
|
| Growth protocol |
HeLa cells were grown in T150 flasks in 25 ml DMEM (Gibco 11965-092), HFF cells were grown in MEM (Gibco 11095-080), and MRC5 cells were grown in a 1:1 mixture of Ham’s F-10 (Gibco 11550-043) and DMEM and all were supplemented with 5% fetal bovine serum (FBS, Gibco 26140-079)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019). Following DFF digestion, nuclei were lightly sonicated for 20s and the soluble material was immunoprecipitated with 2.5 µg of antibodies.
Library construction is detailed in the manuscript.
|
| |
|
| 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, and HCMV (TB40e KF297339.1, Towne FJ616285.1) using bowtie 1.2.2.
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, KF297339.1, FJ616285.1
Supplementary_files_format_and_content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole genomes.
|
| |
|
| Submission date |
Oct 10, 2021 |
| Last update date |
Feb 17, 2022 |
| Contact name |
David Price |
| E-mail(s) |
david-price@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Biochemistry
|
| Lab |
Price Lab
|
| Street address |
500 Newton Road, 260 EMRB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE185618 |
Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq] |
| GSE185763 |
Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes |
|
| Relations |
| BioSample |
SAMN22211572 |
| SRA |
SRX12567766 |
