|
| Status |
Public on Aug 24, 2021 |
| Title |
wild-type_infected_T5d_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Shoots
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: Wild-type
cutivar: Micro-Tom
treatment: Infected
time: T5d
|
| Treatment protocol |
The shoot apex and axillary buds of 17-d-old tomato seedlings of MT and the transgenic line 35S::AtCKX2 were inoculated with 70 µL of 10^6 basidiospores in 0.3% agar-water (w/v), and the plants were kept in a humid chamber for 48 h. Control plants were treated with 0.3% agar-water. Plants were kept under controlled conditions in a growth chamber at 25oC, 14 h photophase and 80% humidity.
|
| Growth protocol |
Wild-type MT and the transgenic line 35S::AtCKX2 were germinated in a 1:1 mixture of substrate:expanded vermiculite and grown under controlled conditions in a growth chamber at 25oC, 14 h photophase and 80% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare Illumina RNA-seq libraries using the KAPA Stranded RNA-Seq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TIS036
|
| Data processing |
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Solanum Lycopersicum ITAG3.1 genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Genome_build: ITAG3.1
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample
|
| |
|
| Submission date |
Jun 26, 2020 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Paulo Teixeira |
| E-mail(s) |
paulojt@usp.br
|
| Phone |
+551934294344
|
| Organization name |
University of São Paulo (ESALQ/USP)
|
| Department |
Biology
|
| Street address |
Av. Pádua Dias, 11
|
| City |
Piracicaba |
| State/province |
SP |
| ZIP/Postal code |
13418-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL25655 |
| Series (1) |
| GSE153345 |
RNA-seq of Solanum lycopersicum cv Micro-Tom (wild-type and 35S::AtCKX2) infected with the fungus Moniliophthora perniciosa |
|
| Relations |
| BioSample |
SAMN15376843 |
| SRA |
SRX8622500 |
