|
| Status |
Public on Oct 21, 2016 |
| Title |
DenV_Input_1_MeRIP |
| Sample type |
SRA |
| |
|
| Source name |
DenV_Input_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 |
SAMN05255979 |
| SRA |
SRX1850526 |
