|
| Status |
Public on May 23, 2024 |
| Title |
Col-0_W+N+_P3ID34_a |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis rosette
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
genotype: Col-0
treatment: W+N+
|
| Treatment protocol |
We use Phenoscope, a high throughput phenotyping robot to apply treatment during the vegetative stage (Tisné et al., 2013). We applied a combination of soil water content (SWC; adjusted with respect to complete soil saturation) and nutrient solution (adjusted to provide a specific amount of nitrate over the course of the experiment : 160.45 ± 7.96 ml of 5mM [Nitrate] nutrient solution in total for the control condition W+N+; 50.85 ± 4.67 ml of 5mM [Nitrate] in total for the single drought stress condition W-N+; 161.93 ± 11.07 ml of 0.5mM [Nitrate] in total for the single N-deficiency condition W+N-; 50.70 ± 4.10 ml of 1.5mM [Nitrate] in total for the combined stress condition W-N-) to establish the different conditions.
|
| Growth protocol |
Seeds were treated with 0.1% agarose and stratified at 4°C in darkness for three days before sowing. Seeds were then sown on unfertilised peat moss soil plugs and transferred to a short-day culture chamber (8 hours photoperiod at 230 μmol.m−2.s−1 light, with days at 21 °C/65%RH and nights at 17 °C/65% RH), where -after 8 days- they were installed on a Phenoscope robot (https://phenoscope.versailles.inra.fr/) for 23 days' culture under 4 different growth conditions. Sampled rosettes have 31 days after sowing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNAs were isolated from the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s recommendations.
RNA-seq libraries were constructed by the POPS platform (IPS2) using the TruSeq Stranded mRNA library prep kit (Illumina®, California, U.S.A.) according to the supplier’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter sequences and bases with a Q-Score below 20 were trimmed out from reads using Trimmomatic (v0.36, Bolger et al. 2014) and reads shorter than 30 bases after trimming were discarded. Reads corresponding to rRNA sequences were removed using sortMeRNA (v2.1, Kopylova E. et al. 2012) against the silva-bac-16s-id90, silva-bac-23s-id98, silva-euk-18s-id95 and silva-euk-28s-id98 databases.
The pipeline combined with hisat2 and feature count was used to align reads against the Arabidopsis thaliana transcriptome Araport11 (Cheng et al., 2017).
The abundance of each gene was calculated by a feature count using the default function.
The percentages of the reads that are successfully mapped to only a single genomic location of the Col-0 genome ranged from 82.19% to 91.92% among accessions. All samples were sequenced and processed following the same process.
Assembly: Araport11
Supplementary files format and content: A text file is submitted with raw gene counts for every gene in every sample
|
| |
|
| Submission date |
Jun 24, 2022 |
| Last update date |
May 23, 2024 |
| Contact name |
Olivier Loudet |
| Organization name |
INRAE
|
| Department |
IJPB
|
| Street address |
Rte de St Cyr
|
| City |
Versailles |
| ZIP/Postal code |
78000 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE206890 |
Multi-omics profiling of 5 Arabidopsis accessions in response to combined water and nitrogen deficiencies |
|
| Relations |
| BioSample |
SAMN29334636 |
| SRA |
SRX15890276 |
