|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on May 08, 2019 |
Title |
1_DAT_Control_2 [RNA-seq] |
Sample type |
SRA |
|
|
Source name |
1_DAT_control_leaf
|
Organism |
Triticum aestivum |
Characteristics |
cultivar: cv Chinese Spring exposed to: Control condition time point: 1 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
|
City |
Ottawa |
State/province |
Ontario |
ZIP/Postal code |
K1A 0C6 |
Country |
Canada |
|
|
Platform ID |
GPL23509 |
Series (2) |
GSE113355 |
MicroRNA-guided regulation of heat stress response in wheat |
GSE113358 |
MicroRNA-guided regulation of heat stress response in wheat |
|
Relations |
BioSample |
SAMN08951071 |
SRA |
SRX3963080 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|