GSE7712   Details

GSE Accession GSE7712
Title Halobacterium NRC-1 Diurnal experiment Light 2
Submission Date 2007-05-04
Last Update Date 2012-03-19
Pubmed ID 18160043
Experiment Type Expression profiling by array
Contributor Kenia,,Whitehead; Nitin,S,Baliga
Contact Name Marc Facciotti
Contact E-mail mfacciotti@systemsbiology.org
Organization Name Institute for Systems Biology
Country USA
Organism Halobacterium salinarum NRC-1
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Organism Synonym
Summary 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 ΟE/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 At each time point, culture was withdrawn by syringe and replaced with nitrogen gas.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 Οg 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 Οl of ULYSIS Alexa Fluor 594 and 6 Οl 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 (Ν) 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
Overall Design 25 conditions were analyzed on duplicate arrays (50 total microarrays) as dye-flips.
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Timepoint Count 25
Timepoints gsm: [1440 minutes, 1620 minutes, 1800 minutes, 1980 minutes, 2160 minutes, 2340 minutes, 2520 minutes, 2700 minutes, 2880 minutes, 3060 minutes, 3240 minutes, 3420 minutes, 3600 minutes, 3780 minutes, 3960 minutes, 4140 minutes, 4320 minutes, 4500 minutes, 4680 minutes, 4860 minutes, 5040 minutes, 5220 minutes, 5400 minutes, 5580 minutes, 5760 minutes]
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