|
Status |
Public on Oct 21, 2016 |
Title |
DenV_IP_2_MeRIP |
Sample type |
SRA |
|
|
Source name |
DenV_IP_MeRIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: Huh7 cell type: liver cell line viral strain: DENV-NGC
|
Treatment protocol |
DENV (MOI 2)
|
Growth protocol |
2 10cm plates of Huh7 cells
|
Extracted molecule |
total RNA |
Extraction protocol |
24 hrs, TRIZOL Illumina Tru-seq PolyA RNA
|
|
|
Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
processed data file: DenV_peaks
|
Data processing |
library strategy: MeRIP-seq Basecalls performed using CASAVA version 1.8.2 PAR-CLIP: Bowtie v1 alignment to human genome hg19 PAR-CLIP: Unaligned reads from step 1 aligned to CA JFH HCV with 2 mismatches PAR-CLIP: PARalyzer v1.1 was applied to step 2 with cluster minimum read depth of 3 reads PAR-CLIP: Background reads (GFP-FL PAR-CLIP) were subtracted from the YTHDF sets topologically MeRIP-seq: STAR version 2.5.0 alignment to combined hg19 and viral genomes MeRIP-seq: Reads aligning to viral genomes were extracted for peak calling MeRIP-seq: the MeRIPPeR peak caller was applied with a minimum peak width of 100 MeRIP-seq: peaks called in two separate replicates for each viral strain were intersected for final calls Genome_build: hg19 Supplementary_files_format_and_content: PAR-CLIP: csv files include PARalyzer output showing YTHDF protein binding clusters on the HCV RNA genome, MeRIP: bed files include peaks called by MeRIPPeR
|
|
|
Submission date |
Jun 16, 2016 |
Last update date |
May 15, 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) |
GSE83438 |
N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection |
|
Relations |
BioSample |
SAMN05255982 |
SRA |
SRX1850529 |