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| Status |
Public on Dec 11, 2023 |
| Title |
YoGI_055_before_heat_stress [B_4] |
| Sample type |
SRA |
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| Source name |
Leaves
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: Leaves
genotype: YoGI_055=CIMMYT, collection accession identifier CWI 13661
treatment: none
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| Treatment protocol |
The heat stress was performed by exposing the plants to 35°C/30°C (day/night) for 14 days after reaching the 3-leaf stage. RNA extraction was conducted before and after stress exposure.
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| Growth protocol |
A total of 13 accessions from Barratt et al., 2023 (Co-expression Network Analysis of Diverse Wheat Landraces Reveals Marker of Early Thermotolerance and Candidate Master-regulator of Thermotolerance Genes) were selected for this work. The seeds (from plants selfed at least three generations) were sown in Levington Advance Seed & Modular F2S compost mixed with Aggregate Industries Garside Sands 16/30 sand (80:20 ratio), treated with CaLypso insecticide. Plants were grown in a Percival AR-75L growth cabinet at 22°C/16°C (day/night) on an 18 hour day/night cycle until reaching the 3-leaves stage.
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| Extracted molecule |
total RNA |
| Extraction 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
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| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Column YoGI_55_Before in processed files
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| Data processing |
Raw reads were then trimmed using Trimmomatic v0.39
Salmon was used to map the trimmed reads to the Triticum aestivum reference genome (IWGSC). Then TxImport was used to input salmon output in R package to generate a table containing transcript abundance, counts, and length from the Salmon quantification files
Assembly: IWGSC V1.1 reference (http://ftp.ensemblgenomes.org/pub/plants/release-46/)
Supplementary files format and content: Salmon output
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| Submission date |
May 12, 2023 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Sara Franco Ortega |
| E-mail(s) |
sara.francoortega@york.ac.uk
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| Organization name |
Centre for Novel Agricultural Products, University of York
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| Department |
Department of Biology
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| Street address |
Wentworth Way
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| City |
Heslington, York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
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| Platform ID |
GPL25409 |
| Series (1) |
| GSE232367 |
Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses |
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| Relations |
| BioSample |
SAMN35056179 |
| SRA |
SRX20304118 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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