|
| Status |
Public on Feb 17, 2022 |
| Title |
12 hpi Flavo PRO-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Primary human foreskin fibroblast (HFF)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HFF
infection (duration and strain): 12 hrs TB40/E
treatment: Flavo
|
| Treatment protocol |
Treatment Protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.
|
| Growth protocol |
HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium (Gibco 11095-080) supplemented with 5% fetal bovine serum (FBS, Gibco 26140-079and grown to confluence for at least one week before infection.
|
| 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).
Library construction is detailed in the manuscript.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: PRO-Seq
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38, and HCMV (TB40e KF297339.1) 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
Supplementary_files_format_and_content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole genomes.
|
| |
|
| Submission date |
Oct 12, 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 |
GPL20301 |
| Series (2) |
| GSE185762 |
Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq] |
| GSE185763 |
Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes |
|
| Relations |
| BioSample |
SAMN22231252 |
| SRA |
SRX12580633 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-KF297339.1-SIC-FW.bw |
507.5 Kb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-KF297339.1-SIC-RV.bw |
548.2 Kb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-combined-dedup.KF297339.1.5prime.FW.SIC.bw |
311.5 Kb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-combined-dedup.KF297339.1.5prime.RV.SIC.bw |
336.1 Kb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-combined-dedup.hg38.5prime.FW.SIC.bw |
16.8 Mb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-combined-dedup.hg38.5prime.RV.SIC.bw |
16.1 Mb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-hg38-SIC-FW.bw |
27.8 Mb |
(ftp)(http) |
BW |
| GSM5623310_2018-08-07-HFF-TB40e-12hpi-Flavo-hg38-SIC-RV.bw |
26.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
