|
Status |
Public on Jan 05, 2022 |
Title |
US1_3hr_2 |
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 deleted US1 open reading frame time: 3hr 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) |
[email protected]
|
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 |
SAMN18475608 |
SRA |
SRX10438283 |