|
| Status |
Public on Jan 03, 2023 |
| Title |
MM-WT-HS-0h Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. Moneymaker background
genotype: WT
tissue: Leaf
treatment: Heat stress 0h
|
| Treatment protocol |
4 weeks old plants were treated at 45°C for 0h and 1h in a climatic chamber (Aralab).
|
| Growth protocol |
Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from 1g of 4-week-old tomato fourth leaves with Nucleospin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 2μg of total RNA using NEBNext Ultra II Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions. RNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bio rep 1
|
| Data processing |
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m" and "samtools markdup -r "
Raw read counts were extracted using featureCounts based on the gene annotations in SollycM82_v1.0.gtf
Differentially expressed genes were identified using R 3.5.1(www.R-project.org) and the package DESeq2 (adj. p value < 0.05)
Assembly: SollycM82_v1.0
Supplementary files format and content: Count matrix of all samples obtained with featureCounts
|
| |
|
| Submission date |
Jun 17, 2022 |
| Last update date |
Jan 03, 2023 |
| Contact name |
Jing An |
| Organization name |
Universite Paris Saclay
|
| Street address |
630 Rue Noetzlin
|
| City |
Paris |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL21762 |
| Series (2) |
| GSE206363 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 2] |
| GSE206365 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions. |
|
| Relations |
| BioSample |
SAMN29179480 |
| SRA |
SRX15782186 |
