|
| Status |
Public on Mar 01, 2022 |
| Title |
Mock-treated shoot rep 1 [C1S] |
| Sample type |
SRA |
| |
|
| Source name |
Mock-treated shoot
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. Moneymaker
age: 15 days post transplantation
treatment: Mock
treatment time: 7 and 14 days post transplantation
tissue: Shoot
|
| Treatment protocol |
Plants were foliarly sprayed with a solution containing 300 µM PA and 0.1 v/v% Tween 20 or a corresponding mock solution at two time points: 7 and 14 days post transplantation.
|
| Growth protocol |
Tomato seedlings (cv. Moneymaker) were routinely germinated, transplanted to individual pots 4 days after germination and placed in a growth chamber (24°C, 16 hours of light)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plants were washed, pooled (4 plants per sample) and root and shoot tissues were ground seperately in liquid nitrogen. RNA was extracted using a Zymo Plant RNA kit as per manufacturer's instructions (Zymo Research).
QuantSeq 3′mRNA-Seq Library Prep Kit (Lexogen) as per manufacturer's instruction, starting from 2 µg RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
4_CON_S1
|
| Data processing |
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to tomato reference genome (ITAG 4.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: ITAG 4.0
Supplementary_files_format_and_content: count table (after normalization using DeSeq2), in .csv format
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Willem Desmedt |
| E-mail(s) |
[email protected]
|
| Organization name |
Ghent University
|
| Department |
Plants and Crops
|
| Lab |
Applied Mycology and Phenomics
|
| Street address |
Valentin Vaerwyckweg 1
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21762 |
| Series (1) |
| GSE167407 |
Transcriptome analysis of piperonylic acid-treated tomato root and shoot tissues |
|
| Relations |
| BioSample |
SAMN18044309 |
| SRA |
SRX10162577 |
