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Sample GSM3104175

Query DataSets for GSM3104175

Status

Public on May 08, 2019

Title

0_DAT_Heat_4 [RNA-seq]

Sample type

SRA

Source name

0_DAT_heat_leaf

Organism

Triticum aestivum

Characteristics

cultivar: cv Chinese Spring
exposed to: 37°C heat stress for 5 days
time point: 0 day after treatment (DAT)
tissue: leaf tissues

Treatment protocol

At the boot stage, a set of 72 plants were exposed to a 37°C heat stress for 5 days while the other 72 plants remained under the control conditions mentioned above. The heat stressed plants were amply watered twice per day during the 5-day stress period to avoid a confounding effect with drought stress.

Growth protocol

A total of 144 Triticum aestivum cv Chinese Spring wheat plants were grown in a PG-40 growth cabinet under long-day conditions of 16 hours of light (300 μmol m−2 s−1) at 18°C and 8 hours of darkness at 16°C. To minimize variation sources, all seeds used in this experiment came from the self-pollination of a single Chinese Spring individual.

Extracted molecule

total RNA

Extraction protocol

Leaf tissue was collected from all heat-stressed and control individual plants immediately at the end of the stress period, i.e., time point zero day after treatment (0 DAT), and at one and four days after treatment (1 and 4 DAT). Total RNA was isolated from all 432 leaf tissue samples using TRI-reagent (Ambion, Naugatuck, CT) as previously described (Ragupathy et al., 2016; Scientific Reports, 6, 39373).
mRNA enrichment, library construction and sequencing were performed by the McGill University and Genome Quebec Innovation Centre (Montreal, QC, Canada). The clustering was done on an Illumina cBot and the flowcell was run on a HiSeq 4000 for 2x100 cycles (paired-end mode) following the manufacturer's instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Adapter sequences were removed using Trimmomatic (Bolger et al., 2014; Bioinformatics, 30, 2114-2120) with parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:55. Adapter-trimmed reads longer than 55 nucleotides were retained.
Reads were mapped to the coding sequences of wheat (IWGSC RefSeq v1.0., 2017) using kallisto (Bray et al., 2016; Nature Biotechnology, 34, 525-527) with default parameters.
Transcripts representing read counts higher than five RPM in at least one library were used for differential expression analysis
Genome_build: Wheat IWGSC RefSeq v1.0., 2017; The assembly and corresponding annotations were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) sequence repository hosted by URGI-INRA https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies and https://wheat-urgi.versailles.inra.fr/Seq-Repository/Annotations
Supplementary_files_format_and_content: Transcript_estimated_read_counts.xlsx

Submission date

Apr 18, 2018

Last update date

May 08, 2019

Contact name

Sylvie Cloutier

E-mail(s)

sylviej.cloutier@canada.ca

Organization name

Agriculture and Agri-Food Canada

Street address

960 Carling Avenue