title: Tavazoie Vora Escherichia coli Affy tiling 2009
status: Public on Sep 01 2009
contact.city: Princeton
contact.first: yirchung
contact.last: Liu
contact.email: yliu@princeton.edu
contact.state: NJ
contact.address: 220 Carl Icahn Laboratory
contact.department: Molecular Biology
contact.country: USA
contact.institute: Princeton University
organism: Escherichia coli
description: The oligonucleotides were based on NC_000913.2.
manufacture_protocol: We designed an Affymetrix tiling array for the MG1655 E. coli genome, containing probes that cover the entire genome at a resolution of 4 bp between steps; however, the steps alternate strand coverage, so there is an 8 bp step between probes on the same strand. There are a total of 2.47 million probes on the array, of which 2,300,160 directly enter analysis as E. coli probe pairs. The Affymetrix system pairs each 25-mer perfect match genomic sequence with a corresponding 25-mer that has a mismatch in the 13th position. The mismatch probe is intended as a cross-hybridization control. In addition to the E. coli sequences, 33,996 probe pairs are sequence-specific controls against other genomes, including B. subtilis, lambda phage, and A. thaliana. The tiling array (Ecoli_Tab520346F) is a standard-sized 200 μL-volume microarray with 5 micron features.