Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 68
Release date: Aug 18 2006
Last update date: Jan 15 2017
Access: Public
Chemicals: Nucleotides
Dataset link An integrated systems approach for understanding cellular responses to gamma radiation.

Experimental Protocol


The wild type strain of Halobacterium salinarium strain NRC-1 was used for the gamma radiation experiments. Culturing of all strains was done in a liquid Complete Medium (CM; at 42 ÂșC with shaking at 220 rpm. Cell pellets from two 180mL cultures (control and experimental) of Halobacterium NRC-1 (OD600nm= 0.4) were resuspended in 1/20 volume in a basal salt solution (CM without peptone) and exposed to 2500 Gy of gamma-ray at 22oC using a 26,000-curie (9.6E14 Bq) 60Co gamma source at Univ. of Maryland College Park Gamma Test Facility at a dose rate of 62.01 Gy/min. Irradiated and control cultures were resuspended in the original volume of CM, split into 20mL aliquots in baffled flasks and incubated at 42oC and 220rpm shaking. Time course samples were placed on ice, pelleted (5000 x g, 4oC, 5 min) and 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. 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 values determined by a maximum likelihood method.

Repositories


GEO

GSE5557

BioProject

PRJNA96059

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Contact


Nitin Baliga

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