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| Status |
Public on Nov 24, 2020 |
| Title |
Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: we aimed to demonstrate the effects of Cycloastragenol on the different plant signaling mechanisms and analyze genome-wide transcriptional responses in order to demonstrate its potential as a new key molecule to help plants overcome different environmental stresses. Methods: RNA-seq was employed to assess transcriptional profiles in treated and non-treated A. thaliana calli. We sequenced two cDNA libraries developed from A. thaliana (wild type Col-0) calli treated with 1µM Cycloatragenol and without. The sequence reads that was filtered, were mapped, aligned and then compared to the reference annotation (the known genes of A. thaliana genome) using Cufflinks tools. Clean data was analyzed using CPC software and results were validated by qRT-PCR using TaqMan and SYBER green assays. Results: We mapped around 63 and 70 million sequence reads from, respectively, control and CAG-treated samples. After filtration and mapping about 21 thousands genes corresponding to an average of 34 thousands transcripts, for each sample were identified. 1045 genes showed differential expression between control and treated sample with a p value < 0.05. Seven genes, which have been chosen randomly, were validated with qRT-PCR. RNA-seq data had a linear relationship with qRT-PCR for a goodness of fit (R2) of 0.959.
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| Overall design |
Transcriptomic response to Cycloastragenol of two samples (Control and 1µM) and an elucidation of the differentially expressed genes in Arabidopsis calli (developed in three biological repetitions for each sample)
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| Contributor(s) |
Mhiri W, Çakır Ö, Turgut-Kara N, Nalbantoğlu B, Ceylan M |
| Citation(s) |
33301486 |
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| Submission date |
Sep 23, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Wissem Mhiri |
| E-mail(s) |
mh.wissem@gmail.com
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| Phone |
+905457404817
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| Organization name |
Yildiz technial university
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| Department |
chemistry
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| Street address |
DAVUTPASA MAH. DAVUTPASA CADDESI ESENLER
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| City |
ISTANBUL |
| ZIP/Postal code |
34220 |
| Country |
Turkey |
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| Platforms (1) |
| GPL24025 |
BGISEQ-500 (Arabidopsis thaliana) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA665188 |
| SRA |
SRP285089 |
