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Status |
Public on Sep 08, 2022 |
Title |
Rosette leaves, Control WT 0 h replicate 1 |
Sample type |
SRA |
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|
Source name |
Rosette leaves
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col-0 Stage: 22-d-old plants line: WT treatment: control 0 h tissue: rosette leaves
|
Treatment protocol |
After 21 days of growth under standard conditions in intermediate day, WT plants and VPZ lines #2 and #4 were exposed to fluctuating light conditions (12h at 23°C and cycles of alternative cycles of 50 µmol photons·m-2·s-1 for 5 min and 500 µmol photons·m-2·s-1 for 1 min / 12h dark at 18 °C ) or under hight light (diurnal light at 500 µmol photons·m-2·s-1). Sampling was carried out at 0 h, 6 h and 30 h by fast harvesting in liquid nitrogen. Transcriptome profiles for Col0 and VPZ lines in each time point and condition were compared to the corresponding sample before treatments.
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Growth protocol |
Arabidopsis thaliana Col-0 and two VPZ lines (#2 and #4) seeds were stratified at 4ºC for 2 days, sown in 9x9 cm pots and cultivated under standard intermediate day conditions [12 h light (125 µmol photons·m-2·s-1) at 22ºC and 12 h darkness at 18ºC].
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from plants was isolated using Trizol and purified using the Direct-zol RNA MiniPrep Plus columns (Zymo Research) according to the manufacturer’s instructions. Generation of mRNA (mRNA-Seq) libraries and sequencing using the paired-end mode were conducted at Novogene Biotech (Beijing, China) with standard Illumina protocols. Libraries were sequenced on an Illumina HiSeq 2500 system. RNA-Seq for First Read unstranded libraries
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
RWT0_1
|
Data processing |
Illumina sequencing reads were generated by Novogene Biotech (Beijing, China). Reads were treated with Trimmomatic to remove adapter sequences, aligned to the Araport11 genome reference with Tophat 2.1.1 and the counts and differential expression files generated with featureCounts/DESeq2. Genome_build: Araport11 Supplementary_files_format_and_content: Excel spread sheet including normalised counts provided according to featureCounts.
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Submission date |
Sep 18, 2019 |
Last update date |
Sep 08, 2022 |
Contact name |
ANTONI GARCIA-MOLINA |
E-mail(s) |
antoni.garcia@cragenomica.es
|
Phone |
0034 686672735
|
Organization name |
Centre for Research in Agrigenomics
|
Department |
Plant Development and Signal Transduction
|
Lab |
Gene regulatory networks in plant development
|
Street address |
Campus UAB - CRAG Building
|
City |
Cerdanyola del Vallès |
State/province |
Barcelona |
ZIP/Postal code |
08193 |
Country |
Spain |
|
|
Platform ID |
GPL17639 |
Series (1) |
GSE137650 |
Comparison of transcript profiles of Arabidopsis WT and VPZ plants to fluctuating light and high light |
|
Relations |
BioSample |
SAMN12781283 |
SRA |
SRX6865371 |