Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 21
Release date: Oct 5 2005
Last update date: Jan 18 2013
Access: Public
Diseases: Tuberculosis
Chemicals: Oxygen, Superoxides
Dataset link Novel Roles of Osteopontin and CXC Chemokine Ligand 7 in the Defense against Mycobacterial Infection

Experimental Protocol


Fluorescence signals for approximately 30,000 spots in slides were detected by fluorescent image analyzer FLA-8000 (Fuji film, Tokyo, Japan) for Cy3 and Cy5, separately. Hybridization intensities were processed using Arrayvision software ver. 6.0 (Imaging Research, Ontario, Canada). Signal and background intensities were determined by the median pixel values. Local background values were determined as the average of four background spots around each gene spot. All spots in the image (for both Cy3 and Cy5 signals) were evaluated for a possibility of dusts, to lower the probability of false data in all experiments. GeneSpring ver. 6.2. (Silicon genetics, Redwood city, CA) was used for data analysis. According to the GeneSpring instruction, normalization of the data was done using "Lowess method" [20]. Spots with dust, or with signal value of which the Cy5 or Cy3 channels were less than three times of background, were excluded.

Repositories


GEO

GSE3408

BioProject

PRJNA93427

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Contact


Vahid Khajoee