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Sample GSM7496514

Query DataSets for GSM7496514

Status

Public on Jun 22, 2023

Title

leaf blade, non-VOC exposed, rep2

Sample type

SRA

Source name

leaf blade

Organism

Zingiber officinale

Characteristics

tissue: leaf blade
genotype: Laiwu variety
treatment: not VOC-exposed

Treatment protocol

See the growth protocol for the description of treatments.

Growth protocol

The effect of P. oligandrum GAQ1 volatile compounds (VOCs) on ginger was evaluated by following the method described by Park et al., (2015). Glass jars containing V8 agar medium were inoculated with a 5 mm actively growing mycelial plug of P. oligandrum whereas the non-inoculated glass jars containing only V8 medium were used as a control. Six small 2 mm holes were made at the bottom of the plastic pots (270 mL) to allow the roots to be exposed to the VOCs produced by P. oligandrum. Two sterilized filter paper pieces (Cat no. 99-102-150, Cytiva, USA) were placed inside the bottom of the plastic pot to avoid the leakage of contaminating liquid through the holes into the glass jar. Equal-sized ginger seedlings were transferred to the plastic pots containing sterilized vermiculite and organic matter (3:1) and placed on the glass jars containing either P. oligandrum or only V8 agar medium as control. The pot-jar assembly was then firmly sealed by wrapping at least nine times with parafilm (PARAFILM M, Bemis, USA) to avoid the escape of VOCs produced by P. oligandrum. The pot-jar assembly was then placed at 16 h light and 8 h dark cycles at 25ºC and watered with sprayer. Plants were watered by wetting the surface of the soil to avoid contamination by leakage of water through holes into the glass jar. Plants were grown for 21 days. Leaf material was collected and frozen at -80°C for subsequent analysis of gene expression. Three replicate samples were collected for each treatment, i.e., three samples for VOCs-exposed and three samples for non-exposed (control) plants. The leaf blades from the two uppermost leaves of the plants grown for 21 days with and without exposure to VOCs were collected, flash-frozen in liquid nitrogen, and stored at -80°C. See publication connected with our GEO submission for images of the ginger plants. Park, Y. S., Dutta, S., Ann, M., Raaijmakers, J. M., and Park, K. (2015). Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds. Biochem. Biophys. Res. Commun. 461, 361–365. doi: 10.1016/j.bbrc.2015.04.039.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantity were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

matrix column name: Control_R2

Data processing

Raw data (raw reads) of fastq format were firstly processed using Trimmomatic (Bolger et al., 2014) and the low-quality reads were removed to obtain the clean reads.
Then, about 48 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the Zingiber officinale reference genome (GCF_018446385.1_Zo_v1.1_genomic.fna) (Cheng et al., 2021) using HISAT2 (Kim et al., 2015) and > 90% of the reads mapped to the genome from all the samples.
FPKM (Roberts et al., 2011) of each gene was calculated using Cufflinks (Trapnell et al., 2010), and the read counts of each gene were obtained by HTSeq-count (Anders et al., 2015).
The GFF file "GCF_018446385.1_Zo_v1.1_genomic.gff " was used.
Assembly: GCF_018446385.1_Zo_v1.1
Supplementary files format and content: tab-delimited text file of read counts for all samples
Supplementary files format and content: tab-delimited text file of FPKM values for all samples

Submission date

Jun 16, 2023

Last update date

Jun 22, 2023

Contact name

Paul Daly

E-mail(s)

[email protected]

Organization name

Jiangsu Academy of Agricultural Sciences

Street address

50 Zhongling St