|
| Status |
Public on Apr 27, 2023 |
| Title |
Diversity of phytoviral RNA U-tailing among ss(+) RNA phytoviruses |
| Organisms |
Spinacia oleracea; Arabidopsis thaliana; Nicotiana benthamiana; Vitis vinifera; Chenopodium quinoa; Nicotiana obtusifolia |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Using 3' RACE-seq method, we analyzed global 3’ terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses.
|
| |
|
| Overall design |
3’ RACE-seq method was used to measure poly(A) tail sizes and analyze uridylation levels. This protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.
|
| Web link |
https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiad278/7161382
|
| |
|
| Contributor(s) |
Joly A, Garcia S, Zuber H, Gagliardi D |
| Citation(s) |
37177985 |
| |
| Submission date |
Aug 30, 2022 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Dominique Gagliardi |
| E-mail(s) |
dominique.gagliardi@ibmp-cnrs.unistra.fr
|
| Organization name |
CNRS
|
| Department |
IBMP
|
| Street address |
12, rue du General Zimmer
|
| City |
Strasbourg |
| ZIP/Postal code |
67084 |
| Country |
France |
| |
|
| Platforms (9)
|
| GPL17970 |
Illumina MiSeq (Arabidopsis thaliana) |
| GPL22072 |
Illumina MiSeq (Nicotiana benthamiana) |
| GPL29591 |
Illumina MiSeq (Vitis vinifera) |
| GPL32609 |
Illumina MiSeq (Chenopodium quinoa; Nicotiana benthamiana; Nicotiana obtusifolia; Vitis vinifera) |
| GPL32610 |
Illumina MiSeq (Nicotiana benthamiana; Vitis vinifera) |
| GPL32611 |
Illumina MiSeq (Spinacia oleracea; Vitis vinifera) |
| GPL32612 |
Illumina MiSeq (Arabidopsis thaliana; Vitis vinifera) |
| GPL32613 |
Illumina MiSeq (Spinacia oleracea) |
| GPL32614 |
Illumina MiSeq (Nicotiana benthamiana; Spinacia oleracea) |
|
| Samples (27)
|
|
| This SubSeries is part of SuperSeries: |
| GSE212358 |
A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns |
|
| Relations |
| BioProject |
PRJNA875112 |
Less...
More...