Halobacterium NRC-1 General transcription factor perturbation
Ontology highlight
ABSTRACT:
ORGANISM(S): Halobacterium sp. NRC-1
SUBMITTER: Nitin Baliga
PROVIDER: E-GEOD-7713 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A predictive model for transcriptional control of physiology in a free living cell.
Bonneau Richard R Facciotti Marc T MT Reiss David J DJ Schmid Amy K AK Pan Min M Kaur Amardeep A Thorsson Vesteinn V Shannon Paul P Johnson Michael H MH Bare J Christopher JC Longabaugh William W Vuthoori Madhavi M Whitehead Kenia K Madar Aviv A Suzuki Lena L Mori Tetsuya T Chang Dong-Eun DE Diruggiero Jocelyne J Johnson Carl H CH Hood Leroy L Baliga Nitin S NS
Cell 20071201 7
The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among approximately 80% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors ...[more]
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE7714: Halobacterium NRC-1 oxygen, light and phr1 perturbation GSE7715: Halobacterium NRC-1 oxygen, light and ura3 perturbation GSE7716: Halobacterium NRC-1 oxygen, light and phr1/phr2 perturbation GSE7717: Halobacterium NRC-1 oxygen, light and bop perturbation GSE7718: Halobacterium NRC-1 oxygen, light and phr2 perturbation GSE7719: Halobacterium NRC-1 oxygen, light and sop2 perturbation GSE7720: Halobacterium NRC-1 oxygen, light and afsQ2 perturbation GSE7721: Halobacterium NRC-1 oxygen, light and htlD perturbation GSE7722: Halobacterium NRC-1 oxygen, light and vng0750C perturbation GSE7723: Halobacterium NRC-1 oxygen, light and boa1 perturbation GSE7724: Halobacterium NRC-1 oxygen, light and ark perturbation GSE7725: Halobacterium NRC-1 oxygen, light and boa4 perturbation GSE7726: Halobacterium NRC-1 oxygen, light and htr1 perturbation GSE7727: Halobacterium NRC-1 oxygen, light and kinA2 perturbation GSE7728: Halobacterium NRC-1 oxygen, light and htr8 perturbation GSE7729: Halobacterium NRC-1 oxygen and light perturbation GSE7730: Halobacterium NRC-1 oxygen, light and phoR perturbation GSE7731: Halobacterium NRC-1 oxygen, light and htr2 perturbation GSE7732: Halobacterium NRC-1 oxygen, light and vng1296C perturbation GSE7733: Halobacterium NRC-1 oxygen, light and vng2334C perturbation GSE7734: Halobacterium NRC-1 oxygen, light and zim perturbation GSE7735: Halobacterium NRC-1 oxygen, light and kinA2 perturbation, experiment 2 GSE7736: Halobacterium NRC-1 oxygen, light and sop2 perturbation, experiment 2 GSE7737: Halobacterium NRC-1 oxygen, light and vng0019h perturbation GSE7738: Halobacterium NRC-1 oxygen, light and gap perturbation Refer to individual Series
2008-01-02 | E-GEOD-7740 | biostudies-arrayexpress
Project description:The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments. For experiment, cultures were started at an OD >> 0.001. Cultures were grown anaerobically at a temperature of 38° C under light:dark cycles (12:12 hrs) for 120 hours then grown under constant light. Average light intensity was 150 μE/m2/sec. Time course sampling began 84 hours into the light:dark phase. Samples were collected every 3 hours for 72 hours. At each time point, culture was withdrawn by syringe and replaced with nitrogen gas. Aliquots of the culture were centrifuged and the cell pellet flash-frozen in a dry ice/ethanol bath after decanting the supernatant. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. For this experiment 3 μl of ULYSIS Alexa Fluor 594 and 6 μl of 660 dyes (Molecular Probes) were used for labeling. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. 25 conditions were analyzed on duplicate arrays (50 total microarrays) as dye-flips.
2010-05-27 | E-GEOD-7712 | biostudies-arrayexpress
Project description:100mM EMS was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of EMS for 30 minutes, cultures were spun down and pellets were re-suspended in same volume of GN101 media. Cultures were then harvested by centrifugation and pellets were snap frozen on a dry-ice ethanol bath. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 samples from EMS perturbed and 8 non-perturbed controls) were analyzed on replicate arrays (dye-flips) all against the same standard reference sample.
2010-05-27 | E-GEOD-7609 | biostudies-arrayexpress
Project description:50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of H2O2 for 30 minutes, cultures were spun down and pellets were resuspended in same volume of GN101 media. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 exposed to H2O2 and 8 non-exposed controls) were each hybridized on duplicate arrays (as dye-flips) against the same standard control sample.
2010-05-27 | E-GEOD-7610 | biostudies-arrayexpress
Project description:Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sub-lethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II). Over 20% of all genes responded transiently within minutes of exposure to Fe(II), perhaps reflecting immediate large scale physiological adjustments to maintain homeostasis. At steady state, each transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up regulation of active efflux of Co(II), Ni(II), Cu(II), and Zn(II), down regulation of Mn(II) uptake and up regulation of Fe(II) chelation, confer resistance to the respective metals. We have synthesized all these discoveries into a unified systems level model to provide an integrated perspective of responses to six transition metals with emphasis on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic potential and regulatory programs of poorly studied organisms. Keywords: stress response, dose response 4 samples were analyzed. Each sample was dye-swapped (2 replicates per condition) and hybridized against a standard control.
2010-06-11 | E-GEOD-7613 | biostudies-arrayexpress
Project description:Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sub-lethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II). Over 20% of all genes responded transiently within minutes of exposure to Fe(II), perhaps reflecting immediate large scale physiological adjustments to maintain homeostasis. At steady state, each transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up regulation of active efflux of Co(II), Ni(II), Cu(II), and Zn(II), down regulation of Mn(II) uptake and up regulation of Fe(II) chelation, confer resistance to the respective metals. We have synthesized all these discoveries into a unified systems level model to provide an integrated perspective of responses to six transition metals with emphasis on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic potential and regulatory programs of poorly studied organisms. Keywords: stress response, dose responseH 4 samples were analyzed. Each sample was dye-swapped (2 replicates per condition) and hybridized against a standard control
2010-06-11 | E-GEOD-7612 | biostudies-arrayexpress
Project description:The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments. Culturing from colony was done in a liquid Complete Medium (CM; at 42 ºC with shaking at 100 rpm). For experiment, cultures were started at an OD >> 0.001. Cultures were grown aerobically (shaking at 100 rpm) and a temperature of 42° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness. Light intensity was 150 μE/m2/sec. Time course sampling began after the 72 hour light:dark phase. Samples were collected every 1 to 3 hours for 65 hours. Aliquots of the culture were centrifuged and the cell pellet flash-frozen in a dry ice/ethanol bath after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR. Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1. Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. 18 conditions were assayed on duplicate arrays (36 total microarrays) as dye flips.
2010-05-27 | E-GEOD-7710 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phoR was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7730 | biostudies-arrayexpress
Project description:The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments. Culturing from colony was done under constant light in a liquid Complete Medium (CM; at 37 ºC with shaking at 220 rpm). For experiment, cultures were started at an OD = 0.005. Cultures were grown aerobically (shaking at 120 rpm) and a temperature of 37° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness. Light intensity was 150 μE/m2/sec. Time course sampling began after the 72 hour light:dark phase. A second culture was also sampled as a control and was grown under complete darkness (no light:dark cycle) before sampling began. Samples from both the experimental and control cultures were collected after 83 hours of exposure to the light:dark cycle every 1 to 3 hours for another 25 hours. Aliquots of the cultures were centrifuged and the cell pellet flash-frozen in liquid nitrogen after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR. Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1. Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 5 μg of RNA from the sample and reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. 24 conditions were analyzed on duplicate microarrays as dye-flips (48 total microarrays).
2010-05-27 | E-GEOD-7711 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletions of phr1 and phr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7716 | biostudies-arrayexpress