Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]
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ABSTRACT:
ORGANISM(S): Halobacterium sp. NRC-1
SUBMITTER: Christopher Plaisier
PROVIDER: E-GEOD-62051 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-10-03 | E-GEOD-62052 | biostudies-arrayexpress
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:A detailed map of genomic locations where TFs bind DNA and modulate transcription is essential to model mechanisms of gene regulation on a systems-scale. Chromatin immunoprecipitation of transcription complexes coupled to microarray (ChIP-chip (Ren et al, 2000)) or sequencing (ChIP-seq (Robertson et al, 2007)) is a commonly used approach to construct such maps. In ChIP-chip, the resolution to which the protein-DNA binding sites (TFBSs) can be identified is often limited by the genomic spacing of the probes in the array. We utilized the MeDiChI algorithm (Reiss et al, 2008) to estimate precise TFBS locations and their corresponding local false discovery rates (LFDRs) from high-resolution arrays for TFBa, TFBd and TFBf. This regression-based method deconvolves the ChIP-chip enrichment ratios along the genome by fitting them with a 'peak profile' model of binding events, assuming a distribution in enriched DNA fragment lengthsÂ. A comparison of the peak intensities derived from MeDiChI for all three TFs (TFBd, TFBf and TFBa) for which there were biological replicate measurements using 2 different microarray platforms (500 nt resolution spotted arrays, see series GSE7045 vs. 13 nt resolution Nimblegen arrays) provided strong validation (with R2 of 0.66, 0.52, and 0.81, respectively) of most TFBSs. Visualizations comparing the two microarray platforms are available at: http://baliga.systemsbiology.net/regulatory_logic/ IP sample of Cmyc tagged TFBs expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample. Three biological replicates for TFBd are available.
2010-05-17 | E-GEOD-15786 | 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:Halobacterium cells, specified general transcription factor knock-out strains or plasmid expressed 6-His tagged general transcription factor strains, were grown to mid-log phase. 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. each knockout or perturbed expression strain was analyzed at a single point during growth. This sample was analyzed on duplicate microarrays as a dye flip (2 microarrays per sample).
2010-05-27 | E-GEOD-7713 | 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