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Status |
Public on Dec 18, 2022 |
Title |
B-treated plant Rep 1 |
Sample type |
SRA |
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Source name |
Finely grounded frozen leaves
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Organism |
Vitis vinifera |
Characteristics |
organ: leaf cultivar: Garnacha Blanca treatment group: B
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Treatment protocol |
The treatments consisted of Akivi at 0.521 g L-1 (Aki), and Bacillus UdG at 108 CFU mL-1 lyophilized (BL) and fresh (BF). A non-treated control (NTC) was included in all the experiments. The products were sprayed on adaxial and abaxial leaf surfaces using an airbrush until near run-off. The experimental design consisted in 4 randomized blocks corresponding to the different treatment modalities (Aki, BL, BF, and NTC), each block was composed of 4 biological replicates of 5 plants.
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Growth protocol |
Garnacha Blanca grapevine cultivars (Vitis vinifera L.) grafted on rootstock 110R, were obtained from commercial nurserie (Agromillora Iberica, Spain). One-year-old bench-grafted grapevine rootlings were planted in a 2 L pot with 80% of the growing media (Prodeasa BV35, Burés Profesional, Spain), 20% of perlite (A-13, Agroteibe, Spain), and 4 g of the fertilizer (Osmocote® Exact Mini 3-4M, ICL Specialty Fertilizers, France). Bench-grafted grapevines were grown in a greenhouse at 25 ± 2ºC, 60 ± 10% relative humidity and a 16:8 h light:dark photoperiod. Young stocks with at least about 4 to 6 expanded leaves were used for the experiments.
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Extracted molecule |
total RNA |
Extraction protocol |
Sampling was carried out 24 h after spraying plants with the products. Four biological replicates were sampled for each treatment for RNA-sequencing analysis (RNA-seq), and three biological replicates for reverse transcription quantitative PCR (RT-qPCR) analysis. Two leaves from each plant (5 plants per repetition) were harvested, grounded, and soaked in liquid nitrogen. Each ground leaf sample was added to 2 mL tubes containing two borosilicate glass beads in order to obtain a fine powder using Tissuelyzer II system (Qiagen, USA) for 1 min at 30 Hz. For total RNA isolation from grapevine leaves, the commercial kit SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, USA) was used following manufacturer’s instructions. Residual DNA was removed using Invitrogen™ TURBO DNA-free™ Kit (Applied Biosystems, USA). The RNA-seq transcriptome library was prepared using the TruSeq Stranded mRNA Sample Prep kit (Illumina, USA) following the manufacturer’s instructions using 1-2 µg of good quality RNA (R.I.N. > 7) as input. The RNA was fragmented 3 minutes at 94°C and every purification step was performed by using 0.81X Agencourt AMPure XP beads. Final libraries were quantified by using the Qubit 2.0 Fluorometer (Invitrogen, USA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies, USA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on paired-end (2x150 bp, 30M reads per sample) at the multiplexing level requested on NovaSeq6000 (Illumina). The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
B_R1a
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Data processing |
Illumina CASAVA v1.8.2 was used for base-calling Raw sequence files were subjected to quality control analysisis using FastQC v0.10.1 Raw sequence files were trimmed and adapters were removed with BBDuk (minimum base quality of 25 and a minimum read length of 35 bp) Reads were mapped against the Vitis vinifera genome with STAR v2.6 Raw expression counts were obtained with FeatureCounts v1.6.1 for each annotated gene using only uniquely mapping reads (MAPQ ≥ 30). Assembly: Vitis vinifera L. genome (Vitis vinifera cv. Pinot noir var. PN40024) (version 12X Ensembl) Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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Submission date |
Aug 15, 2022 |
Last update date |
Dec 18, 2022 |
Contact name |
Mélina Ramos |
E-mail(s) |
melina.ramos66@gmail.com
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Organization name |
University of Girona
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Lab |
CIDSAV
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Street address |
Edifici Jaume Casademont. Porta E, Carrer Pic de Peguera, 15, 4t,
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City |
La Creueta |
State/province |
Girona |
ZIP/Postal code |
17003 |
Country |
Spain |
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Platform ID |
GPL30515 |
Series (1) |
GSE211268 |
Grapevine response to a Dittrichia viscosa extract and a Bacillus velezensis strain |
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Relations |
BioSample |
SAMN30317955 |
SRA |
SRX17075133 |
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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