|
| Status |
Public on Aug 02, 2019 |
| Title |
NCCELBR1-innoculated rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
strain: NC CELBR1
tissue: Leaf
time: 48 hours after innoculation with bacterial spot suspended in water
susceptiblity status: Medium resistance line
|
| Treatment protocol |
Plants were artificially inoculated with Isolate 9 of Xanthomonas perforans, which was found to be extremely virulent. The strain was maintained in pure culture and stored at -80°C. The isolate was grown in Yeast Dextrose Chalk (YDC) agar medium (Lelliott and Stead, 1987) plates for 24-48 hours at 28°C and were overlaid with sterile distilled water and bacteria were dislodged from the plates and the resulting bacterial suspensions were pooled in a sterile glass container. The suspension was standardized by determining its optical density at 600 nm using an Spectrophotometer, and diluted as needed to obtain an OD600 of 0.3 (approximately 2-5×108 CFU/mL). Diluted cells were immediately used for inoculations. The seedlings were sprayed with the bacterial suspension till foliar runoff using a hand sprayer around sunset. Sterile water was used for mock inoculation. Leaf tissue samples after inoculation were collected in liquid nitrogen and stored at -80°C until further processed.
|
| Growth protocol |
Tomato lines were sown in 4P soil mixture (Fafard®, Florida, USA) in 24-cell trays for a greenhouse experiment. Six plants per genotype were planted in two replications in a completely randomized design. Plants were fertilized using a mixture of fertilizer containing a ratio of 20:20:20 of nitrogen, phosphorus, and potassium, respectively. Standard greenhouse treatments for insects and fungal diseases management were used, but copper was not applied to control the bacterial diseases. Humidity near the plants was maintained using humidifiers from 24 hours before inoculation to 48 hours after inoculation and by covering the seedlings with clear plastic.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) followed the protocol for normal insertion size option.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NCCELBR1-IN1
|
| Data processing |
Reads were mapped against tomato Heinz 1706 genome assembly SL3.0 using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools for sorting/indexing
Raw count of reads mapped to annotated gene model (ITAG3.2 version) were extracted using bedtools version 2.25.0
Genome_build: Heinz 1706 genome assembly SL3.0
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample
|
| |
|
| Submission date |
Aug 01, 2019 |
| Last update date |
Aug 02, 2019 |
| Contact name |
Ramsey Lewis |
| E-mail(s) |
rslewis@ncsu.edu
|
| Phone |
(919)-513-4802
|
| Organization name |
North Carolina State University
|
| Department |
Crop and Soil Sciences Department
|
| Lab |
Tobacco Breeding & Genetics
|
| Street address |
101 Derieux PI
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE135232 |
Transcriptome Analysis of Tomato Genotypes in Response to Bacterial spot (Xanthomonas perforans) Race T4 Inoculation |
|
| Relations |
| BioSample |
SAMN12421817 |
| SRA |
SRX6632121 |
