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| Status |
Public on Oct 21, 2016 |
| Title |
N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We use MeRIP-seq and PAR-CLIP in liver cell lines to detail the role of m6A in positive strand RNA virus infection. We find that hepatitis C virus, dengue virus, West Nile virus, yellow fever virus, and Zika virus all contain m6A within their genomes, with some conservation between viruses in methylation sites.
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| Overall design |
Study of m6A methylation in HCV, dengue, WNV, YFV, and Zika virus with two replicates using a polyA prep (m6A antibody, Synaptic Systems; 202 003). Identification of YTHDF1, YTHDF2, YTHDF3 binding sites on the HCV RNA genome using PAR-CLIP
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| Contributor(s) |
Gokhale NS, McIntyre AB, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vasquez C, Willer J, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM |
| Citation(s) |
27773535 |
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| Submission date |
Jun 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
A McIntyre |
| Organization name |
University of Zurich
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| Department |
Molecular Life Sciences
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA325928 |
| SRA |
SRP076674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83438_DenV_peaks.bed.gz |
125 b |
(ftp)(http) |
BED |
| GSE83438_HCV_peaks.bed.gz |
142 b |
(ftp)(http) |
BED |
| GSE83438_M6AHCV_Y1-l15-3.csv.gz |
944 b |
(ftp)(http) |
CSV |
| GSE83438_M6AHCV_Y2-l15-3.csv.gz |
1.4 Kb |
(ftp)(http) |
CSV |
| GSE83438_M6AHCV_Y3-l15-3.csv.gz |
923 b |
(ftp)(http) |
CSV |
| GSE83438_RAW.tar |
10.0 Kb |
(http)(custom) |
TAR (of CSV) |
| GSE83438_WNV_peaks.bed.gz |
102 b |
(ftp)(http) |
BED |
| GSE83438_YFV_peaks.bed.gz |
114 b |
(ftp)(http) |
BED |
| GSE83438_ZikV_Dakar_peaks.bed.gz |
108 b |
(ftp)(http) |
BED |
| GSE83438_ZikV_PR_peaks.bed.gz |
91 b |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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