|
Status |
Public on Nov 28, 2022 |
Title |
WB3 |
Sample type |
SRA |
|
|
Source name |
tomato plant
|
Organism |
Solanum lycopersicum |
Characteristics |
genotype: WT infection: mock
|
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).
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
G10_S10
|
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
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|
|
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 |
SAMN27018506 |
SRA |
SRX14631862 |