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Sample GSM3273401 Query DataSets for GSM3273401
Status Public on May 29, 2019
Title uvr8-2-blue0-R2
Sample type SRA
Source name whole rosette
Organism Arabidopsis thaliana
Characteristics genotype: uvr8-2
developmental stage: 3 weeks old plants
solar treatment: Blue0
tissue: whole rosette
Treatment protocol Outdoors, five filtered sunlight treatments (UVA+B, UVA350, UVA, UV0 and blue0) were created by using different plastic sheets and films as wavelength-selective long-pass optical filters. These treatments were randomly assigned within four blocks or biological replicates. Plants were moved outdoors under filters on 21.08.2014 at sunrise (07:30 to 08:15). Samples from the different filter frames were collected for RNA-seq analysis after 6h of radiation treatment, at solar noon (13:30 to 14:15). The samples were harvested sequentially by block with treatments and genotypes in random order within each block.
Growth protocol Seeds of Arabidopsis wild-type Ler and the photoreceptor mutants uvr8-2 (Brown et al., 2005) and cry1cry2 (Neff and Chory, 1998) were sown in plastic pots (8 × 8 cm) containing a 1:1 mixture of peat and vermiculite and kept in darkness at 4°C for 3 days. Thereafter the pots were transferred to environmentally controlled growth rooms at 23°C/19°C (day/night) and 70%/90% relative humidity under 12 h photoperiod with 280 µmol m−2 s−1 PAR irradiance from white fluorescent lamps. One seedling was transplanted into a new plastic pot (5 × 5 cm) using the same substrate type. After transplanting, plants were kept for 14 days in growth rooms. Rosco filter E-color 226 was used to avoid plants receiving the small amount of UV-A radiation emitted by lamps. Thereafter, five plants/pots from each genotype were randomly assigned to individual plastic trays which were moved outdoors to the filtered sunlight treatments.
Extracted molecule total RNA
Extraction protocol Each biological sample collected consisted of five pooled rosettes frozen in liquid nitrogen and stored at –80°C. The rosette leaves from each pooled sample were ground with mortar and pestle in liquid nitrogen. An aliquote from the powdered sample was separated for gene expression (RNA-seq and qPCR). RNA was extracted with with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). RNA quality and concentration were measured using Agilent 2100 Bioanalyzer and NanoDrop.
RNA-seq library preparation and sequencing was performed at the Institute of Biotechnology, University of Helsinki using two pooled biological replicates. Each replicate consisted of RNA from two different experimental blocks in the field. 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 17, 2018
Last update date May 29, 2019
Contact name Luis Morales
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)
GSE117199 Transcriptome analysis of Arabidopsis thaliana photoreceptor mutants impaired in UV and blue light signaling
BioSample SAMN09668304
SRA SRX4397497

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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