|
| Status |
Public on Jan 05, 2022 |
| Title |
R_6hr_1 |
| Sample type |
SRA |
| |
|
| Source name |
HSV-1 infected HeP2 cells and Drosophila S2 cells
|
| Organisms |
Drosophila melanogaster; Homo sapiens; Human alphaherpesvirus 1 |
| Characteristics |
cell line (human): HeP-2 cells
cell line (drosophila): S2 cells
cell type (human): lung epithelial carcinoma cells
developmental stage (drosophila): late stage embryo
viral infection: HSV-1 (F) strain BAC mutant with repaired US1 open reading frame
time: 6hr
drug treatment: No treatment
|
| Treatment protocol |
Hep-2 cells were infected with the mutant viruses at a MOI of 5 and allowed to progress to 3 or 6 hours post infection. PAA treatment occurred at the time of infection and PAA was maintained in the medium over the course of infection
|
| Growth protocol |
Hep-2 cells were grown and maintained with DMEM 10% fetal bovine serum and the Drosophila S2 cells were grown in Schneider's medium supplemented with 10% NBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were extracted as previously described (Birkenheuer and Baines 2020, Journal of Virology)
nascent RNA was labelled with biotinylated nuclotides during a nuclear run-on. The biotinylated transcripts were isolated and used to prepare sequencing libraries from the reverse transcribed products.
Libraries were constructed as previously described (Mahat and others, 2016, Base-Pair Resolution Genome-Wide Mapping Of Active RNA polymerases using Precision Nuclear Run-On (PRO-seq), Nature Protocols).
Libraries were created using Illumina Index primers for sequencing on the NextSeq550 75 base pair single end sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: PRO-seq
Adapter trimming and processing using Cut Adapt
Raw genome algnments usign BWA
Conversion of BAM files to strand specific BigWigs using kentsource
https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Genome_build: hg38 human genome build, Dm3 Drosophila genome build, HSV-1 (F) strain in-house genome build
Supplementary_files_format_and_content: read count data in BigWig files
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Jan 06, 2022 |
| Contact name |
Joel D Baines |
| E-mail(s) |
jdb11@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
235 Hungerfordhill Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL29914 |
| Series (1) |
| GSE169574 |
ICP22 of Herpes Simplex Virus 1 decreases RNA Polymerase Processivity |
|
| Relations |
| BioSample |
SAMN18475606 |
| SRA |
SRX10438288 |
