redox_geo_template.txt

!Sample_title =  Coordination of frontline defense mechanisms under severe oxidative stress. Array $$ARRAY_ID$$
!Sample_channel_count =  2
!Sample_source_name_ch1 =  Halobacterium salinarum
!Sample_organism_ch1 =  Halobacterium salinarum
!Sample_characteristics_ch1 =  $$CONDITION$$, Strain: NRC-1,  medium: CM
!Sample_biomaterial_provider_ch1 =  Baliga Group, Institute for Systems Biology
!Sample_growth_protocol_ch1 =  Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.
!Sample_molecule_ch1 =  Total RNA
!Sample_extract_protocol_ch1 =  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.
!Sample_label_ch1 =  $$DYE1$$
!Sample_label_protocol_ch1 =  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):1025-35
!Sample_source_name_ch2 =  Halobacterium standard reference sample
!Sample_organism_ch2 =  Halobacterium salinarum
!Sample_characteristics_ch2 =  Strain: NRC-1,  medium: CM
!Sample_biomaterial_provider_ch2 =  Baliga Group, Institute for Systems Biology
!Sample_growth_protocol_ch2 =  Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.
!Sample_molecule_ch2 =  Total RNA
!Sample_extract_protocol_ch2 =  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.
!Sample_label_ch2 =  $$DYE2$$
!Sample_label_protocol_ch2 =  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):1025-35
!Sample_hyb_protocol =  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):1025-35
!Sample_scan_protocol =  ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details
!Sample_description =  Cells incubated under entrainment conditions
!Sample_data_processing =  AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
!Sample_platform_id =  NA
!Sample_contact_name =  NA