title: Progenika P putida KT2440 oligo array
status: Public on Jan 17 2011
contact.city: Hannover
contact.first: Sarah
contact.last: Frank
contact.email: frank.sarah@mh-hannover.de
contact.address: Carl-Neuberg-Str. 1
contact.department: Clinic for Paediatric Pneumology and Neonatology
contact.country: Germany
contact.institute: Medical School Hannover
organism: Pseudomonas putida KT2440
description: The P. putida KT2440 DNA microarray developed contains 5539 oligonucleotides (50-mer) spotted in duplicate onto aminosylane treated 25x75 mm microscope slides, covalently linked to the slide with UV light and heat. The spots, 180 um in diameter, are separated from each other by 265 um and arranged in 48 subarrays (16 columns and 15 rows each). The spotted area is 17x54 mm. The oligonucleotides, designed by BioAlma (www.bioalma.com), are specific for each ORF in the array. These include the 5350 ORFs annotated in the P. putida KT2440 genome (obtained from www.ncbi.nlm.nih.gov, Refseq NC_002947; GenBank accession number AE015451.1), the 140 ORFs defined for the TOL plasmid pWW0 (obtained from www.ncbi.nlm.nih.gov, Refseq NC_003350; GenBank accession number AJ344068.1), and other genes of diverse origins such as commonly used reporter genes (lacZ, gfp) or antibiotic resistance markers. Two oligonucleotides, coding for the rpoD and rpoN genes, respectively, were spotted at 20 different positions of the slide to serve as homogeneity controls. Negative controls (spotting buffer, 50% [vol/vol] dimethylsulfoxide) were spotted in duplicate at 203 positions evenly distributed throughout the printed area. The array was printed by Progenika Biopharma (www.progenika.com).
manufacture_protocol: see manufacturer's web site