Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 2
Release date: May 29 2014
Last update date: Aug 4 2014
Access: Public
Chemicals: Carbohydrates, N-Acetylneuraminic Acid
Genes:
Dataset link Metabolism of sialic acid by Bifidobacterium breve UCC2003

Experimental Protocol


DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p 3 or <0.33 relative to the control.

Repositories


GEO

GSE56291

ArrayExpress

E-GEOD-56291

BioProject

PRJNA242858

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Contact


Mary O'Connell Motherway