A-AFFY-165 - Affymetrix Custom Array Staphylococcus aureus NA-Staph-b520729F tiling microarray

Staphylococcus aureus
The NA-Staph-b520729F tiling microarray was designed in collaboration with Affymetrix (Santa Clara, CA, USA). Specifically, the microarray (format 49-7875 with 11 ��m features) contains a total of 522,406 probes. Since the chip was thought to be used for different applications, it is divided into two parts. The first part corresponds to the tiling sub-array (bpmap files) which contains a total of 384,932 probes (25-mer) which are divided in eight sets. The first set corresponds to 46,310 probes recommend by Affymetrix as controls. The following seven sets are covering both strands of (i) the Staphylococcus aureus NCTC8325 genome (2,821,347 bp covered by 363,127 probes); the S. aureus pathogenicity islands (ii) SaPI1 (15,229 bp covered by 1,892 probes), (iii) SaPI2 (14,753 bp covered by 1,897 probes), (iv) SaPIbov1 (15,887 bp covered by 1,978 probes), (v) SaPIbov2 (27,031 bp covered by 3,356 probes); (vi) the staphylococcal chromosomal cassette SCC mecIV-ACMEI (54,947 bp covered by 6,938 probes) and (vii) the phage 80a (43,859 bp covered by 5,744 probes). Each 25-mer probe was tiled each 14-nt across the whole genome, resulting in 11-nt overlaps and a 7-nt offset of the tile between strands. This design enables a 7-nt resolution for hybridization of double stranded targets and an 14-nt resolution for strand-specific targets. The second part of the chip corresponds to the S. aureus gene expression sub-array (cdf file) which contains 91,164 probes grouped into 3,224 probe sets (each probe set includes 14 perfect match and 14 mismatch probes). 3,122 probe-sets are targeting unique S. aureus genes while 102 probe-sets are controls recommended by Affymetrix. The BPMAP file is available for download on the ArrayExpress FTP site.
Alejandro Toledo-Arana (alejandro.toledo@unavarra.es);Affymetrix, Inc. (support@affymetrix.com)
All experiments done using A-AFFY-165: (E-MEXP-2778, E-MEXP-3924)
Array DesignA-AFFY-165.adf.txt