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Sample GSM3267806 Query DataSets for GSM3267806
Status Public on Jul 01, 2020
Title Shahdara.control_I
Sample type SRA
 
Source name Shahdara.control_whole rosette
Organism Arabidopsis thaliana
Characteristics genotype/variation: Shahdara
developmental stage: 3 weeks old plants
treatment: control
tissue: whole rosette
Treatment protocol Three weeks old plants were exposed with 350 nL L-1 ozone and control clean air for two hours.
Growth protocol Seeds were sown on 1:1 peat: vermiculite, stratified at 4°Cfor three days in the dark, and then grown at 22°C/19°C for a week. Subsequently four geminated seedlings were transplanted into 8 × 8 cm pots containing new 1:1 peat: vermiculite mixture. The pots were randomly placed into a controlled chamber (Weiss Bio1300; Weiss Gallenkamp), where plants were grown at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.
Extracted molecule total RNA
Extraction protocol Four rosettes per genotype from control and ozone treatment were pooled, frozen into liquid nitrogen and stored at -80°C. Three biological replicates of RNA were isolated with with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). RNA quality and concentration were measured using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared using 1µg total RNA following instructions from Illumina TruSeq Stranded mRNA Library Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The quality of raw reads was first inspected in Chipster using FastQC.
Removal of adapter sequences and trimming and cropping of the reads was done using Trimmomatic-0.33 (Bolgert et al., 2014) in single-end mode. The bases with a quality score less than 20 were trimmed from the beginning and the end of the sequences, and the reads shorter than 30 bases were removed from the analysis (-phred33, LEADING:20, TRAILING:20 and MINLEN:30).
Filtered reads were mapped to the Arabidopsis transcript reference database AtRTD2 (Zhang et al., 2017) using Kallisto V-0.43.0 (CMD:quant) (Bary et al., 2016) with 4000 bootstrap sets. The final count table for each biological replicate was obtained as the mean of the bootstrap runs.
Genome_build: Arabidopsis transcript reference database AtRTD2
Supplementary_files_format_and_content: Matrix-table including gene counts for each sample
 
Submission date Jul 12, 2018
Last update date Jul 01, 2020
Contact name Luis Morales
E-mail(s) luis.morales@oru.se
Phone +46 19 301033
Organization name Örebro University
Department School of Science and Technology
Street address Fakultetsgatan 1
City Örebro
ZIP/Postal code SE-70182
Country Sweden
 
Platform ID GPL19580
Series (1)
GSE117052 Transcriptome analysis of apoplastic reactive oxygen species signaling in Arabidopsis thaliana accessions with varying ozone sensitivity.
Relations
BioSample SAMN09652298
SRA SRX4386876

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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