|
| Status |
Public on May 09, 2019 |
| Title |
denv_48h_1_IP |
| Sample type |
SRA |
| |
|
| Source name |
Huh7 liver cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
viral strain: DENV2-NGC
library strategy: MeRIP-seq
time point: 48 hours
treatment: infected
antibody: NEB anti-m6A antibody
|
| Growth protocol |
Huh7 cells were grown in DMEM (Mediatech) supplemented with 10% fetal bovine serum (HyClone), 25 mM HEPES, and 1X non-essential amino acids (Thermo Fisher Scientific) and seeded in 15 cm plates prior to infection
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIzol
Illumina Tru-seq PolyA RNA,1 x 50
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
denv_48h_1.macs2_peaks.narrowPeak
|
| Data processing |
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8.2
STAR version 2.5.0 alignment to combined hg38 and viral genome reference (using the appropriate virus genome depending on sample)
Peaks identified using MACS2 version 2.1.1 with effective genome size scaled to the transcriptome (1e8)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files (bed)
|
| |
|
| Submission date |
May 08, 2019 |
| Last update date |
May 09, 2019 |
| Contact name |
A McIntyre |
| Organization name |
University of Zurich
|
| Department |
Molecular Life Sciences
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE130891 |
MeRIP-seq for host response to Flaviviridae infection |
|
| Relations |
| BioSample |
SAMN11604646 |
| SRA |
SRX5806900 |
