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| Status |
Public on Jul 31, 2007 |
| Title |
Halobacterium NRC-1_oxygen_response_timecourse_set3 |
| Organism |
Halobacterium salinarum NRC-1 |
| Experiment type |
Expression profiling by array
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| Summary |
In order to ensure the reproducibility of the transcriptional response of Halobacterium NRC-1 to oxic/anoxic transitions, we repeated global mRNA measurements for the oxygen time series data in GSE5924, except that cultures were equilibrated to low oxygen for 24 hours prior to the start of the experiment rather than 12 hours, and time course sampling continued to 12 hours post-shift to high oxygen rather than stopping at 6 hours. The results of these data suggest that there is good reproducibility between datasets, and that Halobacterium responds robustly to oxic/anoxic transitions.
Keywords: time course
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| Overall design |
This experiment was a replicate of Oxygen time series 1, except that cells were equilibrated at low oxygen for 24 hours prior to the experiment start. Also, time course sampling was more frequent after the shift to high oxygen and sampling was continued beyond 6 hours to 12 hours. Halobacterium sp. NRC-1 (ATCC700922) was routinely grown in complex medium (CM; 250g/L NaCl, 20g/L MgSO4.7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) at 37ºC under full-spectrum white light. For turbidostat experiments, starter cultures of NRC-1 were inoculated into 2L of CM in a 3.0 L vessel (5-10% inoculum) and grown to mid-logarithmic phase (OD600 ~ 0.5) in batch mode in a BioFlo100 modular bench top fermentor (New Brunswick Scientific, Edison, NJ) at 300 rpm, pH 7.0. Prior to each experiment, an oxygen sensor (model InPro 6000, Mettler Toledo, Columbus, OH) was calibrated to 100% oxygen at 1200rpm and sparging with 3.2 VVM of air. These conditions were approximately equivalent to oxygen saturation in CM medium, which is 1.6 mg/L (~5uM). Once the culture reached mid-logarithmic phase, the oxygen level was rapidly decreased to ~0-0.5% within 5-10 minutes (achieved by cutting off airflow and decreasing agitation to 250 rpm), and allowed to incubate under anoxic conditions for 24 h prior to the start of sampling. The oxygen concentration in the culture was then rapidly increased to approximately 85-100% (achieved by agitating at 1100 rpm and sparging with air at 3.2 VVM) and sampling commenced and continued at the times indicated in the Sample records. The culture was subsequently maintained in high oxygen conditions for 12hr. During these perturbations, all other parameters were kept constant (pH 7.2-7.3, 37ºC, ambient light, O.D.600~0.5-6.5). Each culture sample taken at the times indicated in the Sample records was split in half, one half being used for RNA extraction and the other for ATP measurement.
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| Contributor(s) |
Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van P, Hohmann L, Baliga NS |
| Citation(s) |
17785531 |
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| Submission date |
Apr 19, 2007 |
| Last update date |
Jan 15, 2017 |
| Contact name |
Amy K Schmid |
| E-mail(s) |
aschmid@systemsbiology.org
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| Fax |
206-1299
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| Organization name |
Institute for Systemsbiology
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| Lab |
Nitin Baliga Halobacterium Lab
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| Street address |
1441 N 34th St
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
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| Platforms (1) |
| GPL3739 |
ISB Halobacterium Spotted Microarray |
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| Samples (36)
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| GSM183356 |
Halobacterium_oxygen3_LO2_-05min, Array 10684 |
| GSM183357 |
Halobacterium_oxygen3_LO2_-05min, Array 10638 |
| GSM183358 |
Halobacterium_oxygen3_L2H_000min, Array 10639 |
| GSM183359 |
Halobacterium_oxygen3_L2H_000min, Array 10640 |
| GSM183360 |
Halobacterium_oxygen3_H_005min, Array 10641 |
| GSM183361 |
Halobacterium_oxygen3_H_005min, Array 10642 |
| GSM183362 |
Halobacterium_oxygen3_H_010min, Array 10643 |
| GSM183363 |
Halobacterium_oxygen3_H_010min, Array 10644 |
| GSM183364 |
Halobacterium_oxygen3_H_020min, Array 10645 |
| GSM183365 |
Halobacterium_oxygen3_H_020min, Array 10646 |
| GSM183366 |
Halobacterium_oxygen3_H_030min, Array 10647 |
| GSM183367 |
Halobacterium_oxygen3_H_030min, Array 10648 |
| GSM183368 |
Halobacterium_oxygen3_H_045min, Array 10649 |
| GSM183369 |
Halobacterium_oxygen3_H_045min, Array 10656 |
| GSM183370 |
Halobacterium_oxygen3_H_060min, Array 10657 |
| GSM183371 |
Halobacterium_oxygen3_H_060min, Array 10658 |
| GSM183372 |
Halobacterium_oxygen3_H_090min, Array 10659 |
| GSM183373 |
Halobacterium_oxygen3_H_090min, Array 10660 |
| GSM183374 |
Halobacterium_oxygen3_H_120min, Array 10663 |
| GSM183375 |
Halobacterium_oxygen3_H_120min, Array 10664 |
| GSM183376 |
Halobacterium_oxygen3_H_180min, Array 10665 |
| GSM183377 |
Halobacterium_oxygen3_H_180min, Array 10666 |
| GSM183378 |
Halobacterium_oxygen3_H_240min, Array 10685 |
| GSM183379 |
Halobacterium_oxygen3_H_240min, Array 10686 |
| GSM183380 |
Halobacterium_oxygen3_H_300min, Array 10687 |
| GSM183381 |
Halobacterium_oxygen3_H_300min, Array 10670 |
| GSM183382 |
Halobacterium_oxygen3_H_360min, Array 10671 |
| GSM183383 |
Halobacterium_oxygen3_H_360min, Array 10672 |
| GSM183384 |
Halobacterium_oxygen3_H_420min, Array 10673 |
| GSM183385 |
Halobacterium_oxygen3_H_420min, Array 10688 |
| GSM183386 |
Halobacterium_oxygen3_H_540min, Array 10675 |
| GSM183387 |
Halobacterium_oxygen3_H_540min, Array 10676 |
| GSM183388 |
Halobacterium_oxygen3_H_600min, Array 10677 |
| GSM183389 |
Halobacterium_oxygen3_H_600min, Array 10678 |
| GSM183390 |
Halobacterium_oxygen3_H_660min, Array 10679 |
| GSM183391 |
Halobacterium_oxygen3_H_660min, Array 10682 |
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| Relations |
| BioProject |
PRJNA99361 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE7559_RAW.tar |
39.2 Mb |
(http)(custom) |
TAR (of CSV) |
| Processed data included within Sample table |
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