|
| Status |
Public on Nov 28, 2022 |
| Title |
MA2 |
| Sample type |
SRA |
| |
|
| Source name |
tomato plant
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: bsk830-1 mutant
infection: P. fluorescens
|
| Treatment protocol |
Total RNA was isolated with the RNeasy Plant Mini Kit (QIAGEN) from leaves of wild-type and bsk830-1 tomato plants infected by vacuum with a suspension of P. fluorescens or mock-inoculated (three biological replicates for each treatment, in total 12 samples collected at 6 h post-inoculation). RNA integrity was evaluated using the 4200 TapeStation System (Agilent Technologies).
|
| Growth protocol |
CRISPR/Cas9-generated tomato BSK830 mutant lines were impaired in ROS accumulation induced by the flg22 and flgII-28 flagellin epitopes. In addition, in wild-type plants the flagellin deficient Pseudomonas syringae pv. tomato (Pst) strain DfliC developed larger populations than wild-type Pst bacteria, whereas in BSK830 mutants Pst wild-type and DfliC bacteria displayed a similar growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Plant Mini Kit (QIAGEN) followed by mRNA libraries construction
RNA-Seq cDNA libraries were prepared from the RNA samples using the NEBNext Ultra™ II mRNA Library Prep Kit for Illumina and then PCR amplified using NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
G2_S2
|
| Data processing |
Partek® Flow® 8.0
Bases were trimmed on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign STAR - 2.7.3a to Solanum lycopersicum SL3.0 assembly (NCBI genome assembly ID 393272)
Quantification to transcriptome performed using Partek E/M algorithm.
Assembly: Solanum lycopersicum SL3.0 assembly (NCBI genome assembly ID 393272)
Supplementary files format and content: Sobol_tomato_NormRPKM_SolycID
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Nov 28, 2022 |
| Contact name |
Metsada Pasmanik-Chor |
| E-mail(s) |
metsada@tauex.tau.ac.il
|
| Organization name |
Tel Aviv University
|
| Department |
Biology
|
| Lab |
Bioinformatics Unit
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE199518 |
The tomato receptor-like cytoplasmic kinase Fir1 is involved in flagellin signaling and regulates pre-invasion immunity |
|
| Relations |
| BioSample |
SAMN27018511 |
| SRA |
SRX14631857 |
