|
| Status |
Public on May 26, 2015 |
| Title |
Total RNA - mock Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: foreskin
cell type: fibroblasts
time post infection: mock
infection reagent: mock
|
| 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 |
SAMN02935363 |
| SRA |
SRX660439 |
