|
| Status |
Public on Oct 31, 2023 |
| Title |
TFP_Clodano_S_biol rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Floral bud tetrad stage
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Floral bud tetrad stage
genotype: Clodano
treatment: Stressed
replicate: biol rep3
|
| Treatment protocol |
For heat-stress treatments, the plants at bolting stage have been submitted during 3 weeks to a mean temperature of 35°C during the day (16h) and 25°C during the night (8h) using the main and two auxiliary heaters and the temperature has been monitored all along the HS. In both conditions, the hygrometry was around 55% all day and plants had a daily watering.
|
| Growth protocol |
Plant material consisted in of five different tomato (Solanum lycopersicum) cultivars: Clodano (Syngenta™), DRK7024 (De Ruiter™), JAG8810 (Bayer™), M82 and West Virginia 106 (WVA106). In NS conditions, plants were cultivated in a greenhouse with a photoperiod of 16h/8h with a mean temperature of 24°C during the day and a mean temperature of 18°C during the night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5-10 floral buds for each stage were sampled before and 20 days after the start of the heat stress from 20-25 plants per genotype for the RNAseq analysis (Figure S1B). Total RNAs were isolated from 200 and 500 mg of floral buds at different developmental stages using TRIzol Reagent (Life Technologies). Total RNA extract was purified with the Qiagen RNAeasy mini kit RNA. After DNase treatment (DNA-free Kit, Life Technologies), the total RNA quantity and quality (RNA integrity number, RIN) were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA extracts with a RIN of 10 were used for sequencing.
The RNA libraries were constructed as described in the Illumina TruSeq Stranded mRNA guide. mRNAs were sequenced in a HiSeq 3000 sequencing system with 2 × 125 bp paired-end sequences (Illumina HiSeq SBS Kit v4) by the Genotoul bioinformatics platform, Toulouse (http://bioinfo.genotoul.fr/index.php).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
raw reads were trimmed with trimgalore
trimmed reads were mapped using STAR
raw read count was made using featurecounts
Assembly: SLYMIC v1.0 - Solanum lycopersicum - Micro-Tom cultivar https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_012431665.1/
Supplementary files format and content: tab-delimited text includes raw count for per sample
|
| |
|
| Submission date |
Oct 26, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Anis Djari |
| E-mail(s) |
anis.djari@toulouse-inp.fr
|
| Organization name |
INPT
|
| Street address |
6 All. Emile Monso
|
| City |
Toulouse |
| ZIP/Postal code |
31400 |
| Country |
France |
| |
|
| Platform ID |
GPL23294 |
| Series (1) |
| GSE246372 |
Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress |
|
| Relations |
| BioSample |
SAMN38001233 |
| SRA |
SRX22242244 |
