|
| Status |
Public on Dec 12, 2017 |
| Title |
tomato not inoculated rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
4-week old plants mature leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype/variation: cv Heinz
treatment: healthy
|
| Treatment protocol |
Mature leaves of 4 week-old Arabidopsis thaliana and Solanum lycopersicum (Heinz genotype) were inoculated or not with the S. sclerotiorum strain 1980. An agar plug (5mm in diameter) containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves and plants were maintained at 80% humidity
|
| Growth protocol |
Plants were grown in Jiffy pots under controlled conditions at 22°C, with a 9 hour light period and a light intensity of 120 µmol/m2/s 4 weeks prior to infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The edge of developed necrotic lesions (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
HiSeq control software 2.2.38, RTA 1.18.61.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: TAIR10 (A. thaliana) - version 3 (S. lycopersicum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Nov 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sylvain Raffaele |
| E-mail(s) |
sylvain.raffaele@inrae.fr
|
| Organization name |
INRA
|
| Lab |
LIPM
|
| Street address |
28 chemin de borde rouge
|
| City |
Castanet tolosan |
| ZIP/Postal code |
31320 |
| Country |
France |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE106811 |
Global transcriptome of Arabidopsis thaliana and Solanum lycopersicum infected by S. sclerotiorum |
|
| Relations |
| BioSample |
SAMN08015223 |
| SRA |
SRX3385264 |
