{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Marc Facciotti"],"organism":["Halobacterium sp. NRC-1"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-7725"],"description":["A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa4 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-123","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-124","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-130","Growth Protocol - Halobacterium NRC-1 ura3 and boa4 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM) and in dark (painted flask).","Growth Protocol - Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-126","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-125","Growth Protocol - Halobacterium NRC-1 ura3 and boa4 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM) and in light.","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-124","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-123","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-129","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-128","Growth Protocol - Halobacterium NRC-1 ura3 and boa4 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-127","Nucleic Acid Extraction - Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-129","Growth Protocol - Halobacterium NRC-1 ura3 and boa4 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-127","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-128","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-125","Hybridization - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-130","Labeling - see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-126"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - AnalyzerDG software for spotfinding. see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details","Assay Data Transformation - ID_REF =  VALUE = normalized log 10 ratio (treatment/reference) with FLAG=K removed RATIO = standard ratio (not log10) X_INT = Background subtracted, normalized intensity value of channel 1 Y_INT = Background subtracted, normalized intensity value of channel 2 FLAG = Internal Quality Control Flag(s) UNF_VALUE = normalized log10 ratio (treatment/reference)","Image Adquisition - ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["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 (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments-suggesting a remarkable degree of network completeness. Using this model we have constructed and tested hypotheses critical to this organism's interaction with its changing hypersaline environment. This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments."],"study_type":["transcription profiling by array"],"species":["Halobacterium sp. NRC-1"],"pubmed_title":["A predictive model for transcriptional control of physiology in a free living cell."],"pubmed_authors":["Nitin Baliga","Min Pan","Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS","Marc Facciotti"],"additional_accession":[]},"is_claimable":false,"name":"Halobacterium NRC-1 oxygen, light and boa4 perturbation","description":"A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa4 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.","dates":{"release":"2008-01-03T00:00:00Z","modification":"2023-10-03T14:35:30.448Z","creation":"2022-03-14T19:39:07.552Z"},"accession":"E-GEOD-7725","cross_references":{"GEO":["GSE7725"],"pubmed":["18160043"],"EFO":["EFO_0002768"],"doi":["10.1016/j.cell.2007.10.053"]}}