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| Status |
Public on Feb 01, 2024 |
| Title |
Transcriptional response of Gemmatimonas phototrophica to changing light regimes [AP64_LowLight] |
| Organism |
Gemmatimonas phototrophica |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
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| Overall design |
G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of each experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown in triplicates aerobically in the dark until reaching approx. OD600 = 0.2. Then cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1. Sampling was done 2, 4, and 8 hours after the light was switched on. Control cultures were kept in dark and sampled for each time point as a reference.
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| Contributor(s) |
Kopejtka K, Tomasch J, Shivaranu S, Saini MK, Kaftan D, Koblížek M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 16, 2024 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Karel Vaclav Kopejtka |
| E-mail(s) |
kopejk00@alga.cz
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| Phone |
+420777623254
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| Organization name |
Institute of Microbiology Czech Acad. Sci.
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| Department |
Centre Algatech
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| Lab |
Laboratory of Anoxygenic Phototrophs
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| Street address |
Novohradska
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| City |
Trebon |
| ZIP/Postal code |
37981 |
| Country |
Czech Republic |
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| Platforms (1) |
| GPL32851 |
Illumina NovaSeq 6000 (Gemmatimonas phototrophica) |
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| Samples (21)
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| GSM8019115 |
AP64, 2 hours after the shift to light, rep1 |
| GSM8019116 |
AP64, 2 hours after the shift to light, rep2 |
| GSM8019117 |
AP64, 2 hours after the shift to light, rep3 |
| GSM8019118 |
AP64, 2 hours after the shift to light, dark control rep1 |
| GSM8019119 |
AP64, 2 hours after the shift to light, dark control rep2 |
| GSM8019120 |
AP64, 2 hours after the shift to light, dark control rep3 |
| GSM8019121 |
AP64, 4 hours after the shift to light, rep1 |
| GSM8019122 |
AP64, 4 hours after the shift to light, rep2 |
| GSM8019123 |
AP64, 4 hours after the shift to light, rep3 |
| GSM8019124 |
AP64, 4 hours after the shift to light, dark control rep1 |
| GSM8019125 |
AP64, 4 hours after the shift to light, dark control rep2 |
| GSM8019126 |
AP64, 4 hours after the shift to light, dark control rep3 |
| GSM8019127 |
AP64, 8 hours after the shift to light, rep1 |
| GSM8019128 |
AP64, 8 hours after the shift to light, rep2 |
| GSM8019129 |
AP64, 8 hours after the shift to light, rep3 |
| GSM8019130 |
AP64, 8 hours after the shift to light, dark control rep1 |
| GSM8019131 |
AP64, 8 hours after the shift to light, dark control rep2 |
| GSM8019132 |
AP64, 8 hours after the shift to light, dark control rep3 |
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| Relations |
| BioProject |
PRJNA1065381 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE253351_RAW.tar |
1.2 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
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