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Series GSE133321 Query DataSets for GSE133321
Status Public on Aug 03, 2020
Title Expression profiling by small RNA-seq for identifying miRNA associated with sound vibration in plant
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed an expression profiling basd on small RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.
 
Overall design A group of plants was prepared to be expose to sound vibration (SV, 10 kHz) at 90 dB every 3 h for 10 days. The other group of plants with non-treatment were also prepared as a control group. Then, all samples were drenched with a pathogen (R. solanacearum). miRNA quantification data were generated by performing small RNA-seq analysis of 18 arabidopsis samples, which were obtained at 0d, 1d and 2d after dreching pathogen. Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).
 
Contributor(s) Kim J, Kim S, Jung J, Ryu C
Citation(s) 32973716
Submission date Jun 26, 2019
Last update date Sep 28, 2020
Contact name Seon-Kyu Kim
E-mail(s) seonkyu@kribb.re.kr
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (18)
GSM3905722 0D_10-2_1_miRNA-seq
GSM3905723 0D_10-3_1_miRNA-seq
GSM3905724 0D_10-4_1_miRNA-seq
This SubSeries is part of SuperSeries:
GSE133325 Identifying genes associated with sound vibration in plant
Relations
BioProject PRJNA551116
SRA SRP212095

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133321_RAW.tar 70.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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