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Sample GSM4083729 Query DataSets for GSM4083729
Status Public on Sep 08, 2022
Title Rosette leaves, Control WT 0 h replicate 1
Sample type SRA
 
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.
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
 
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.
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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