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| Status |
Public on Nov 01, 2018 |
| Title |
Exploring the sound-modulated delay in tomato ripening through expression analysis of RNA. |
| Organism |
Solanum lycopersicum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We evaluated the molecular mechanism underlying this delaying fruit ripening by performing RNA-sequencing analysis of tomato fruits at 6 h, 2 days (d), 5 d and 7 d after 1 kHz sound vibration treatment. Differentially expressed genes revealed that some of these genes are involved in plant hormone and cell wall modification processes. Ethylene and cytokinin biosynthesis and signalling genes were downregulated by sound vibration treatment, whereas genes involved in flavonoid, phenylpropanoid and glucan biosynthesis were upregulated. Our results indicate that sound vibration helps delay fruit ripening through the sophisticated regulation of RNAs and transcription factor genes.
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| Overall design |
Total RNA was isolated using an RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR. Sequencing was performed on paired end reads (2×150 bp) using the HiSeq-2000 platform (Illumina).
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| Contributor(s) |
Kim S, Kim J, Jung J, Ryu C, Jeong M |
| Citation(s) |
30010774 |
| Submission date |
Oct 30, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
| |
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| Platforms (1) |
| GPL16345 |
Illumina HiSeq 2000 (Solanum lycopersicum) |
|
| Samples (24)
|
| GSM2836228 |
Sound wave treated tomato fruit Tomato-1KHZ_2D_01 |
| GSM2836229 |
Sound wave treated tomato fruit Tomato-1KHZ_2D_02 |
| GSM2836230 |
Sound wave treated tomato fruit Tomato-1KHZ_5D_01 |
| GSM2836231 |
Sound wave treated tomato fruit Tomato-1KHZ_5D_02 |
| GSM2836232 |
Sound wave treated tomato fruit Tomato-1KHZ_6H_01 |
| GSM2836233 |
Sound wave treated tomato fruit Tomato-1KHZ_6H_02 |
| GSM2836234 |
Sound wave treated tomato fruit Tomato-1KHZ_7D_01 |
| GSM2836235 |
Sound wave treated tomato fruit Tomato-1KHZ_7D_02 |
| GSM2836236 |
Control tomato fruit Tomato-CTRL_2D_01 |
| GSM2836237 |
Control tomato fruit Tomato-CTRL_2D_02 |
| GSM2836238 |
Control tomato fruit Tomato-CTRL_5D_01 |
| GSM2836239 |
Control tomato fruit Tomato-CTRL_5D_02 |
| GSM2836240 |
Control tomato fruit Tomato-CTRL_6H_01 |
| GSM2836241 |
Control tomato fruit Tomato-CTRL_6H_02 |
| GSM2836242 |
Control tomato fruit Tomato-CTRL_7D_01 |
| GSM2836243 |
Control tomato fruit Tomato-CTRL_7D_02 |
| GSM3327805 |
Sound wave treated tomato fruit Tomato-1KHZ_2D_03 |
| GSM3327806 |
Sound wave treated tomato fruit Tomato-1KHZ_5D_03 |
| GSM3327807 |
Sound wave treated tomato fruit Tomato-1KHZ_6H_03 |
| GSM3327808 |
Sound wave treated tomato fruit Tomato-1KHZ_7D_03 |
| GSM3327809 |
Control tomato fruit Tomato-CTRL_2D_03 |
| GSM3327810 |
Control tomato fruit Tomato-CTRL_5D_03 |
| GSM3327811 |
Control tomato fruit Tomato-CTRL_6H_03 |
| GSM3327812 |
Control tomato fruit Tomato-CTRL_7D_03 |
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| Relations |
| BioProject |
PRJNA416331 |
| SRA |
SRP122938 |
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