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Sample GSM5591990

Query DataSets for GSM5591990

Status

Public on Sep 23, 2021

Title

Zax3_+P_Sh_2hr

Sample type

SRA

Source name

rice seedling

Organism

Oryza sativa

Characteristics

tissue: Shoot
treatment: Zaxinone
timepoint: 2hr

Treatment protocol

three-week-old seedlings were grown hydroponically in half-strength modified Hoagland nutrient solution. Seedlings were further treated with 5 µM zaxinone for 2 h, 6 h, or 24 h and tissues were collected.

Growth protocol

Nipponbare background WT rice plants were grown under controlled conditions (a 12 h photoperiod, 200-µmol photons m-2 s-1 and day/night temperature of 27/25 oC). Rice seeds were surface-sterilized in a 50 % sodium hypochlorite solution with 0.01 % Tween-20 for 15 min. The seeds were rinsed with sterile water and germinated in the dark overnight. The pre-germinated seeds were transferred to petri dishes containing half-strength liquid Murashige and Skoog (MS) medium and incubated in a growth-chamber for 7 days. Thereafter, the seedlings were transferred into black falcon tubes filled with half-strength modified Hoagland nutrient solution with adjusted pH to 5.8. The nutrient solution consisted of 5.6 mM NH4NO3, 0.8 mM MgSO4.7H2O, 0.8 mM K2SO4, 0.18 mM FeSO4.7H2O, 0.18 mM Na2EDTA.2H2O, 1.6 mM CaCl2.2H2O, 0.8 mM KNO3, 0.023 mM H3BO3, 0.0045 mM MnCl2.4H2O, 0.0003 mM CuSO4.5H2O, 0.0015 mM ZnCl2, 0.0001 mM Na2MoO4.2H2O and 0.4 mM K2HPO4.2H2O.

Extracted molecule

total RNA

Extraction protocol

Total rice root RNA was extracted with TRIzol (Invitrogen, https://www.thermofisher.com/de/de/home.htmL) using a Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA).
The cDNA libraries were constructed following standard Illumina protocols and paired‐end sequenced on an Illumina HiSeq 4000 machine by the Bioscience core lab of KAUST.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

Zax

Data processing

RNA‐Seq reads were aligned to the O. sativa genome v7.0 downloaded from Phytozome v12.1 (http://phytozome.jgi.doe.gov/).
Data processing and analysis were performed using the LSTrAP workflow. Adapter sequences were removed from fastq files by Trimmomatic, and aligned to the genome using HISAT2.
Read counts aligned to each annotated gene were computed with HTSeq. The results were passed through LSTrAP quality control and TPM normalized. The mean data were used to cluster and resistance level was visualized as a heatmap using a hierarchical clustering R script. Principal component analysis (PCA), a multivariate statistical technique, was further conducted to examine links between samples.
All analyses were performed using R statistical package. For differential gene expression, read counts from HTSeq were analyzed using the R package DESeq2. Genes were considered differentially expressed based on a P‐value adjusted by the Benjamini–Hochberg procedure below 0.05.
Supplementary_files_format_and_content: Differential gene expression analysis

Submission date

Sep 21, 2021

Last update date

Sep 23, 2021

Contact name

Jian You Wang

E-mail(s)

jianyou.wang@kaust.edu.sa

Phone

0543907951

Organization name

KAUST