|
| Status |
Public on Dec 14, 2022 |
| Title |
TGA2.1-NahG_control_PVY_2 [OE358] |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Solanum tuberosum |
| Characteristics |
genotype: TGA2.1-NahG
transgenic line: 7
treatment: control
inoculation: PVY
sampling: lesions with surrounding area
number of sections in pool: 8
|
| Treatment protocol |
Three to four weeks old potato plants were inoculated with GFP-tagged infectious PVY clones or mock inoculum. To induce gene overexpression, plants were treated with dexamethasone (DEX) foliar spray solution, containing 30 mM DEX and 0.01 % (v/v) Tween-20, or control spray solution without DEX (control), 3 h prior to virus inoculation, 3 h after virus inoculation and every day post inoculation until sampling.
|
| Growth protocol |
Plants were propagated from stem node tissue cultures and transferred to soil two weeks after node segmentation, where they were kept in growth chambers under controlled environmental conditions at 22/20 °C with a long-day (16 h) photoperiod of light (light intensity 4000 lm/m2) and 60-70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Early visible lesions and their immediate surrounding area were sampled from PVY-inoculated leaves four days post inoculation. Sections of comparable size were sampled from mock-inoculated leaves as controls. Three plants per genotype per treatment were analysed, pooling together all lesions or mock-sections from one leaf per plant. Tissue sections were stored in RNA-later RNA Stabilization Solution (ThermoFisher Scientific) and then homogenized using Tissue Lyser (Qiagen). Total RNA was isolated with TRIzol (Invitrogen) and Direct-zol RNA MicroPrep Kit, DNAse treated and purified with RNA Clean & Concentrator kit (both Zymo Research) according to the manufacturer’s instructions.
Strand-specific library preparation was performed by Novogene (HongKong) using standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read quality control was performed using FastQC (Andrews, 2010).
The presence of contaminant organism reads was determined using Centrifuge (Kim et al., 2016).
Reads were mapped to the reference potato genome and counted using STAR (Dobin et al., 2013) with default parameters.
Differential expression analysis was performed in R using the limma package (Smyth et al., 2018).
Genome_build: Phureja DM1-3 potato genome v4.04 (Xu et al., 2011) using the merged PGSC and ITAG genome annotation (Petek et al., 2020)
Supplementary_files_format_and_content: differential gene expression statistics, normalized and raw read counts table in Excel spreadsheet format
|
| |
|
| Submission date |
Feb 03, 2022 |
| Last update date |
Dec 14, 2022 |
| Contact name |
Marko Petek |
| E-mail(s) |
marko.petek@nib.si
|
| Organization name |
National Institute of Biology
|
| Department |
Department of Biotechnology and Systems Biology
|
| Street address |
Večna pot 111
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL27910 |
| Series (1) |
| GSE196078 |
Differential gene expression in salicylic acid-deficient transgenic plants overexpressing StTGA2.1 after viral infection. |
|
| Relations |
| BioSample |
SAMN25638873 |
| SRA |
SRX14035767 |
