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| Status |
Public on Oct 10, 2023 |
| Title |
Azotobacter vinelandii str. DJ transcriptomic time-course under nitrogenase derepressing conditions |
| Organism |
Azotobacter vinelandii DJ |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Comparison of Azotobacter vinelandii str. DJ transcriptomes using either ammonium or dinitrogen as sole nitrogen source. Transcriptomes from cells in early stages of nitrogenase derepression (10 min and 30 min) and at the peak of nitrogenase derepression (4 hours) were compared against the corresponding controls from cells using ammonium as nitrogen source. Kinetics of the nitrogen fixation (nif) genes expression profiles resemble those previously published (Poza-Carrion, 2013; doi: 10.1128/jb.00942-13).
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| Overall design |
Azotobacter vinelandii str. DJ were cultivated in Burk’s modified medium at 30°C with or without nitrogen sources. For nitrogenase derepression experiments (diazotrophic growth conditions), NH4+ grown cells were diluted in fresh NH4+ containing medium at an optical density at 600 nm (OD600) of 0.005 and further cultivated for 17 h. Cells were then collected by centrifugation, washed with NH4+ free or NH4+ containing medium (control cultures), and resuspended in the same medium at a final OD600 of 0.5. Cells were then incubated at 30°C with shaking (200 rpm) in independent Erlenmeyer flasks. At different times, samples were collected and RNA it´s isolated from the cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of different growth condition at three time points.
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| Contributor(s) |
Rubio LM, Poza-Carrión C |
| Citation(s) |
37998022 |
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| Submission date |
Oct 05, 2023 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Luis M. Rubio |
| E-mail(s) |
luis.rubio@csic.es
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| Organization name |
Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC)
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| Street address |
Campus de Montegancedo UPM. Crta. M-40 km 38
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| City |
Madrid |
| ZIP/Postal code |
28223 |
| Country |
Spain |
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| Platforms (1) |
| GPL33825 |
Illumina HiSeq 2000 (Azotobacter vinelandii DJ) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA1024529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE244772_RPKM_counts.txt.gz |
199.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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