|
| Status |
Public on Apr 19, 2023 |
| Title |
HA-ICP22 cells, salt stress, DOX, replicate 2 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
HA-ICP22 cells, salt stress, DOX, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line
time post infection: no infection
agent: no infection
treatment: DOX (5 μg/mL) + KCl (80 mM)
|
| Treatment protocol |
HFFF cells were infected for 15 minutes with HSV-1 strain F or ICP22-null virus at an MOI of 10 followed by PBS wash and media replacement. 350 µg/ml PAA was added to indicated samples for 8 or 12 hours. 5 μg/mL DOX was added to indicated samples 48 hours prior to collecting RNA. 80 mM KCl (salt stress) was added to indicated samples for 2 hours prior to collecting RNA.
|
| Growth protocol |
Human fetal foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected at 60-80% confluency 24h after the last split. T-HF cells were cultured in DMEM supplements with 10% FBS and P/S. Expression of HA-ICP22 and HA-ICP22 + V5-ICP27 was induced by adding 5 μg/ml doxycycline for 48h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat
35bp paired-end, NextSeq 500 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Total RNA prepared using Trizol
HA_ICP22_Salt_stress_plus_DOX_RNA_2
|
| 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 v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene read counts
|
| |
|
| Submission date |
Oct 04, 2021 |
| Last update date |
Apr 19, 2023 |
| 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 |
GPL18573 |
| Series (1) |
| GSE185239 |
The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (RNA-seq) |
|
| Relations |
| BioSample |
SAMN22035828 |
| SRA |
SRX12471349 |
