|
| Status |
Public on Jun 14, 2021 |
| Title |
WT-Xg_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Fla. 8000
genotype: Wild-type
age: 6 weeks
tissue: Leaf
treatment: Xanthomonas gardneri
time after treatment: 6h
|
| Treatment protocol |
Four individual plants of each genotype (wild type, Sldmr6-1.1 and Sldmr6-1.2 mutants) were used for RNA sequencing. Two leaves from each plant were syringe-infiltrated with a mock solution (10 mM MgCl2) or with a X. gardneri strain 153 suspension (OD600=0.25). Samples were harvested six hours after infiltration.
|
| Growth protocol |
Wild type and mutant (Sldmr6-1.1 and Sldmr6-1.2) plants were grown on soil (Miracle-Gro Supersoil Potting Soil) in a growth chamber at 25°C under a 16h light/8h dark photoperiod. The experiment was performed with six-week-old plants.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma, STRN250).
RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library prep kit (Illumina 20020594).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
BSDT001F2
BSDT_counts.txt
|
| Data processing |
Illumina bcl2fastq v2.20.0 was used for basecalling.
Illumina adapters and low-quality reads were removed from the sequenced libraries using Trim Galore v0.6.4.
The filtered reads were aligned to the reference genome (SL 4.0) using STAR v2.6.1c.
The featureCounts function (v 1.6.3) from the subread package was used to count reads that mapped to protein-coding genes.
Genome_build: SL 4.0/ITAG 4.0
Supplementary_files_format_and_content: BSDT_counts.txt: Tab-delimited text file including read counts per gene for each sample.
|
| |
|
| Submission date |
Aug 30, 2020 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Daniela Paula de Toledo Thomazella |
| E-mail(s) |
dthomazella@gmail.com
|
| Organization name |
UC Berkeley
|
| Department |
PMB/IGI
|
| Lab |
Staskawicz Lab
|
| Street address |
2151 Berkeley Way
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL25655 |
| Series (1) |
| GSE157154 |
Transcriptional response of wild type and dmr6 mutants of tomato to Xanthomonas gardneri |
|
| Relations |
| BioSample |
SAMN15944685 |
| SRA |
SRX9038631 |
