title: Lactobacillus acidophilus NCFM whole genome 7K oligoarray [4 reps]
status: Public on Mar 24 2009
contact.city: Raleigh
contact.first: Todd
contact.middle: Robert
contact.last: Klaenhammer
contact.email: trk@ncsu.edu, yjgoh@ncsu.edu, sjoflahe@ncsu.edu
contact.state: NC
contact.department: Department of Food, Bioprocessing, and Nutrition Sciences
contact.country: USA
contact.institute: North Carolina State University
contact.phone: 919-515-2972
organism: Lactobacillus acidophilus NCFM
description: A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) were spotted on glass slides.  Each oligo (representing each gene) was spotted 4 times in a random pattern.  To assess the reliability of the platform, we conducted a microarray hybridization experiment labeling cDNA from the same RNA sample with Cy3 and Cy5.  Hybridization data revealed a linear correlation (R value) in the relative expression level of  0.98 of 11,520 spots
manufacture_protocol: OligoArray 2.1 (Rouillard et al., 2003) was selected based on literature, availability (free software for academic use), and user-friendly accessibility for oligonucleotide design.  The oligonucleotide length range was set to 60-70 nt, the melting temperature (Tm) range to 80-96°C and the GC content range to 25-50% according to the GC content of the NCFM genome (34.71%). The thresholds to reject oligonucleotides that can form stable secondary structures and to start to consider putative cross-hybridizations were both set to 65°C. Oligonucleotides containing either AAAAA, TTTTT, GGGGG, CCCCC or longer homopolymers were rejected.  A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) meeting the above criteria were obtained. No primers could be obtained for 41 genes mainly due to the presence of prohibited sequences (homopolymers). Twenty-four of the oligonucleotides obtained were unspecific.  Oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA).