GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE244772 Query DataSets for GSE244772
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
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).
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.
Contributor(s) Rubio LM, Poza-Carrión C
Citation(s) 37998022
Submission date Oct 05, 2023
Last update date Jan 11, 2024
Contact name Luis M. Rubio
Organization name Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC)
Street address Campus de Montegancedo UPM. Crta. M-40 km 38
City Madrid
ZIP/Postal code 28223
Country Spain
Platforms (1)
GPL33825 Illumina HiSeq 2000 (Azotobacter vinelandii DJ)
Samples (6)
GSM7829444 DJ,10m, NH4-
GSM7829445 DJ,10m, NH4-, plus 15m Ammonium Shock
GSM7829446 DJ,30m, NH4-
BioProject PRJNA1024529

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE244772_RPKM_counts.txt.gz 199.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap