{"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-7723"],"description":["A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa1 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 Ag"],"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):1025-112","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):1025-113","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):1025-110","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):1025-111","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):1025-109","Growth Protocol - Halobacterium NRC-1 ura3 and boa1 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.","Growth Protocol - Halobacterium NRC-1 ura3 and boa1 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).","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):1025-114","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):1025-113","Growth Protocol - Halobacterium NRC-1 ura3 and boa1 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):1025-112","Growth Protocol - Halobacterium NRC-1 ura3 and boa1 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):1025-108","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):1025-107","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):1025-109","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):1025-107","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):1025-108","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):1025-111","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):1025-110","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):1025-114"],"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":["Metabolomics","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 hyp"],"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 boa1 perturbation","description":"A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa1 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 Ag","dates":{"release":"2008-01-03T00:00:00Z","modification":"2023-09-22T09:33:54.42Z","creation":"2022-03-14T22:47:17.659Z"},"accession":"E-GEOD-7723","cross_references":{"GEO":["GSE7723"],"pubmed":["18160043"],"EFO":["EFO_0002768"],"doi":["10.1016/j.cell.2007.10.053"]}}