|
Status |
Public on May 26, 2015 |
Title |
Total RNA - 8hpi Rep 1 |
Sample type |
SRA |
|
|
Source name |
Total RNA
|
Organism |
Homo sapiens |
Characteristics |
tissue: foreskin cell type: fibroblasts time post infection: 8 h p.i. infection reagent: Herpes simplex virus 1, strain 17
|
Treatment protocol |
Cells were infected for 10 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.
|
Growth protocol |
Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was prepared using Trizol. Newly transcribed RNA was purified as described in Rädle et al., JoVE 2013. TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (only for total RNA). No rRNA depletion was performed for the 4sU-RNA samples!
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Total RNA prepared using Trizol
|
Data processing |
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.3.0 RPKM values were calculated based on the total number of reads mapping to the human genome. Genome_build: hg19, JN555585 Supplementary_files_format_and_content: text files with RPKM values
|
|
|
Submission date |
Jul 23, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Caroline Friedel |
Organization name |
Ludwig-Maximilians-Universität München
|
Department |
Institut für Informatik
|
Street address |
Amalienstr. 17
|
City |
München |
ZIP/Postal code |
80333 |
Country |
Germany |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE59717 |
Wide-spread disruption of transcription termination in HSV-1 infection: Next generation sequencing of total and newly transcribed (4sU-RNA) RNA |
|
Relations |
Reanalyzed by |
GSE97009 |
BioSample |
SAMN02935353 |
SRA |
SRX660429 |