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| Status |
Public on Dec 31, 2023 |
| Title |
Transcriptomic analysis of salt stress responsive genes related pigment metabolism in photoheterotrophic Arabidopsis calli |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In order to investigate the salt stress induced chlorophyll biosynthesis-related genes in photoheterotrophic cultures, we performed RNA-Seq analysis on A. thaliana calli exposed to 100 mM NaCl on MS medium containing 0.5 mg/L 2,4-D 30 days. Four different conditions of samples were sequenced on Illumina HiSeq Platform in total and generated about 4.49 Gb per sample. The average genome and gene mapping rates were 93.52% and 90.78%, respectively. According to expression profile analysis, some DEGs demonstrated altered related to chlorophyll pigment metabolism. According to analysis, green callus color of photoheterotrophic calli were mainly connected with the induction of LHCB4.3 light harvesting complex photosystem II (Gene ID:818599), AT1G49975 photosystem I reaction center subunit N (Gene ID: 841421), PAM68 PAM68-like protein (DUF3464) (Gene ID: 2745715) and AT3G63540 thylakoid lumenal protein (Mog1/PsbP/DUF1795-like photosystem II reaction center PsbP family protein)(Gene ID: 7922413) genes. Furthermore, 8 DEGs were randomly selected to validate the transcriptome profiles via qPCR. These results will provide a foundation for further studies aimed at giving photosynthetic properties to in vitro plant cultures.
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| Overall design |
Morphological observation and total RNA-Seq analysis of pigment formation under NaCl treatment in Arabidopsis thaliana (Col-0)
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/37133632/
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| Contributor(s) |
Çelik H, Arıkan B, Çakır Ö, Uçarlı C, Kara NT |
| Citation(s) |
37133632 |
| Submission date |
Nov 15, 2021 |
| Last update date |
Mar 31, 2024 |
| Contact name |
Haluk Çelik |
| E-mail(s) |
halukcelik93@gmail.com
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| Organization name |
Istanbul University
|
| Street address |
İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü
|
| City |
ISTANBUL |
| State/province |
Vezneciler |
| ZIP/Postal code |
34134 |
| Country |
Turkey |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA780468 |
| SRA |
SRP346129 |
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