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SRX20304139: GSM7329464: YoGI_155_after_heat_stress [A_25]; Triticum aestivum; ssRNA-seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 20.7M spots, 6.2G bases, 1.9Gb downloads

External Id: GSM7329464_r1
Submitted by: Department of Biology, Centre for Novel Agricultural Products, University of York
Study: Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses
show Abstracthide Abstract
Climate change is not only causing a rise of global temperature but also more variable climates. In major wheat-producing countries, spring temperatures have increased up to 40°C in recent years. Considering the wheat optimal growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. To combat this threat, it is imperative to understand the response of wheat to early heat stress. This research is focus on understanging the transcriptional reprogramming of wheat when exposed to heat stress during the three-leaf stage. Differential expression and weighted gene co-expression network analysis have been used here before and after the stress to to identify candidate master-regulators of this transcriptional response. Overall design: Thirteen wheat landraces where used to asses the wheat transcriptomic response to 14-days heat stress during the early stages of development (3-leaf stage). The experiment was performed by growing the plant until 3 leaf-stage (22°C/16°C (day/night) on an 18 hour day/night cycle) and then submitting the plants to 14 days of 35°C/30°C (day/night) and three days of recovery (22°C/16°C (day/night) on an 18 hour day/night cycle) after that. Four replicates, per treatment, per landrace accession were used in this experiment. mRNA-Seq analysis was performed on RNA material collected at the 3-leaf stage and after the heat stress.
Sample: YoGI_155_after_heat_stress [A_25]
SAMN35056188 • SRS17629315 • All experiments • All runs
Library:
Name: GSM7329464
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: For each one of the 13 wheat accessions, 2 cm of leaf tissue was taken at the 3-leaf stage and after the 14 days of heat stress. Total RNA was extracted from <100 mg of individual leaf tissue samples using the E.Z.N.A Plant RNA Kit (Omega Bio-Tek, ) including a DNase treatment, according to the manufacturer's protocol. RNA concentration was quantified by both NanoDrop ND-1000 Spectrophotometer, and Qubit 4 Fluorometer and the quality was assessed by Agilent Technology 2100 Bioanalyzer. Samples with RNA Integrity Number (RIN) values >7 were used for the sequencing. Replicates were pooled into 1 sample per accession, per group, at equimolar proportions. The library preparation and sequencing were performed by Novogene UK. The library was obtained using TruSeq Stranded mRNA (Illumina) . The mRNA was purified using poly-T oligo attached magnetic beads, fragmented and the first strand cDNA synthesized using random hexamer primers, whilst the second strand cDNA using dUTP for directional library. End-repair, A-tailing, adapter ligation, size selection,USER enzyme digestion to remove the UTP-containing second strand cDNA, PCR amplification and purification TruSeq stranded mRNA run in the Illumina Novaseq 6000 platform (Illumina, CA, USA) with an 150bp paired-end sequencing strategy
Runs: 1 run, 20.7M spots, 6.2G bases, 1.9Gb
Run# of Spots# of BasesSizePublished
SRR2451989420,746,1096.2G1.9Gb2023-12-12

ID:
27725311

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