|
| Status |
Public on Jan 16, 2019 |
| Title |
Nucleotide resolution of RNA polymerase II transcription in human cytomegalovirus |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). Unmapped reads were then mapped to HCMV (Genbank FJ616285.1) (track hub available at https://github.com/P-TEFb/trackHub_HCMV).
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| |
|
| Overall design |
TB40/E: PRO-Seq on uninfected HFF treated with 0.1% DMSO 1 h, or 4 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h. Towne: PRO-Seq and PRO-Cap on uninfected or 96 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h.
|
| Web link |
https://journals.asm.org/doi/10.1128/mBio.02047-18
|
| |
|
| Contributor(s) |
Nilson KA, Parida M, Ball CB, Price DH, Li M, Meier JL |
| Citation(s) |
30755505 |
| |
| Submission date |
Apr 19, 2018 |
| Last update date |
Sep 22, 2022 |
| Contact name |
David H Price |
| E-mail(s) |
david-price@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Biochemistry
|
| Lab |
260 EMRB
|
| Street address |
500 Newton Road
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (13)
|
| GSM3104909 |
PRO-Seq of uninfected DMSO-treated HFF (TB40/E) |
| GSM3104910 |
PRO-Seq of 4 h infected DMSO-treated HFF (TB40/E) |
| GSM3104911 |
PRO-Seq of 4 h infected flavopiridol-treated HFF (TB40/E) |
| GSM3104912 |
PRO-Seq of uninfected DMSO-treated HFF (Towne) |
| GSM3104913 |
PRO-Seq of uninfected flavopiridol-treated HFF (Towne) |
| GSM3104914 |
PRO-Seq of 96 h infected DMSO-treated HFF (Towne) |
| GSM3104915 |
PRO-Seq of 96 h infected flavopiridol-treated HFF (Towne) |
| GSM3104916 |
PRO-Cap of uninfected DMSO-treated HFF (Towne) |
| GSM3104917 |
PRO-Cap of uninfected flavopiridol-treated HFF (Towne) |
| GSM3104918 |
PRO-Cap of 96 h infected DMSO-treated HFF (Towne) |
| GSM3104919 |
PRO-Cap of 96 h infected flavopiridol-treated HFF (Towne) |
| GSM3613769 |
PRO-Seq of infected 96 h DMSO-treated HFF (Towne BAC) |
| GSM3613770 |
PRO-Seq of infected 96 h flavopiridol-treated HFF (Towne BAC) |
|
| Relations |
| BioProject |
PRJNA451016 |
| SRA |
SRP141182 |
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