|
| Status |
Public on Apr 18, 2022 |
| Title |
Control_24h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: leaf
genotype: cv. Better Bush
treatment: Control_24h
|
| Treatment protocol |
Six tomato plants were infested with 6 larvae deposited on the three terminal leaflets of the 3rd true leaf and six control plants were subject to mock deposition. Two harvests were conducted after 5 h and 24 h of herbivory. At both harvest time, the infested leaflets from which the larvae have been removed (and the corresponding leaflets of the control plant) were sampled, immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Twelve sequencing libraries were created corresponding to 4 conditions in triplicates (Tuta infested 5h and 24h; control 5h and 24h)
|
| Growth protocol |
Tomato plants (cv. Better Bush) were grown on a Nutrient Film Technique system set in a growth chamber (16h photoperiod, 23°C/18°C day/night in air and 23°C in nutrient solutions, 60% air humidity)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using EZNA Plant RNA kit mini plus kit (Omega bio-tek, Norcross, GA, USA). Three micrograms of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were processed and filtered using the Trimmomatic software
they were mapped on the tomato genome (ITAG2.4) using the BWA-MEM software
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using FeatureCounts software
Assembly: tomato genome (ITAG2.4)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 14, 2022 |
| Last update date |
Apr 19, 2022 |
| Contact name |
Romain Larbat |
| E-mail(s) |
romain.larbat@univ-lorraine.fr
|
| Organization name |
LAE
|
| Department |
INRAE
|
| Street address |
2 avenue de la forêt de Haye
|
| City |
Vandoeuvre les nancy |
| ZIP/Postal code |
54500 |
| Country |
France |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE200795 |
Transcriptomic analysis of the tomato plant response to Tuta absoluta herbivory |
|
| Relations |
| BioSample |
SAMN27584797 |
| SRA |
SRX14852908 |
