|
| Status |
Public on Feb 10, 2021 |
| Title |
leave48at22 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaves
age: 15 days
genotype: Tolerant
treatment: High pH 8.3
extraction time: 48h
|
| Treatment protocol |
Treatments were applied in 15 day-old plants growing on hydroponics. Control (½ Hoagland solution at pH 5.9), high pH (½ Hoagland solution at pH 8.3), and bicarbonate (½ Hoagland solution at pH 8.3 and 10 mM NaHCO3). Solutions were buffered with different proportions of MES and BTP depending on final pH
|
| Growth protocol |
Selected seeds were surface sterilized by soaking in 70% (v/v) ethanol for 1 min, suspended in 30% (v/v) commercial Clorox bleach and 1 drop of Tween-20 for 5 min and rinsed 5 times in sterile 18 MΩmilli-Q water.Seeds were sown in 0.2 ml tubes containing 0.6 % agar prepared in nutrient solution 1/2 Hoagland, pH 5.9. Seeds were kept at 4 °C for 7 days in the dark to synchronize germination. After 10 days in the growth chamber (12h light/12h dark, 150 µmol cm−2·s−1, 40% humidity and 25 °C) the bottom of the tubes containing seedlings was cut off and the tubes were placed in 150 ml hydroponic content, containing aerated nutrient solution 1/2 Hoagland, pH 5.9. When 15 days old, the seedlings were separated in different sets and the following treatments were applied.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf material from plants cultivated under hydroponic conditions was recollected at 3 and 48 hours after initiating the treatments.Leaves were immersed in liquid nitrogen, homogenized to a fine powder, and stored at -80º C. The total RNA of 100 mg of leaf powder for each biological replicate was extracted using the Maxwell® plant RNA kit (Promega Corporation,WI, USA) following the manu-facturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq. Library preparation was perform using Novogene protocol. Sequence reads: 150 bp-Illumina reads, paired-end, unstranded. Number of analyzed reads: 30-47 million pairs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
leave48at22
|
| Data processing |
Raw Illumina quality control read was performed using FASTQC software.
Each paired set of two fastq files were first processed and Reads containing adaptor- or vector-derived sequences were removed using Trim Galore!
Cleaned reads together with the transcriptome of Arabidopsis thaliana were used to quantify gene expression at transcript level using the software Salmon. v0.9.1
Design Formula, Construction of the DESeq2 Object and Collapse of Technical Replicates. DESeq R package (1.18.0)
The resulting p-values were adjusted using the Benjamini and Hochberg’s approach [29] for controlling the false discovery rate (FDR). To perform a definitively list of DGEs, genes were filtered by adj pvalue (adjusted p-value) <0.05 and LFC >1 and LFC <-1.
Genome_build: Arabidopsis thaliana reference transcriptome file used: Arabidopsis_thaliana.TAIR10.cdna.all.fa
Supplementary_files_format_and_content: Matrix table with clean and normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 10, 2021 |
| Last update date |
Feb 10, 2021 |
| Contact name |
Laura Pérez-Martín |
| Organization name |
Universitat Autònoma de Barcelona
|
| Department |
Biologia animal biologia vegetal i ecologia
|
| Lab |
Fisiologia vegetal
|
| Street address |
Cerdanyola del Vallès
|
| City |
Cerdanyola del Vallès |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE164502 |
Title: Leaf transcriptomics of Catalan A. thaliana demes under alkaline and carbonated stress at 3h and 48 hours. |
|
| Relations |
| BioSample |
SAMN17274429 |
| SRA |
SRX9816516 |
