Array Design Name	Affymetrix Custom Array Staphylococcus aureus NA-Staph-b520729F tiling microarray 
Comment[AdditionalFile:BPMAP]	NA-Staph_tiling(-)strand.bpmap
Comment[AdditionalFile:BPMAP]	NA-Staph_tiling(+)strand.bpmap
Comment[AdditionalFile:TXT]	A-AFFY-165.design_file.txt
Comment[ArrayExpressReleaseDate]	2011-06-24
Comment[ArrayExpressSubmissionDate]	2011-06-24 15:42:03
Comment[Organism]	Staphylococcus aureus
Provider	Alejandro Toledo-Arana (alejandro.toledo@unavarra.es);Affymetrix, Inc. (support@affymetrix.com)
Comment[ArrayExpressAccession]	A-AFFY-165
Comment[Description]	The NA-Staph-b520729F tiling microarray was designed in collaboration with Affymetrix (Santa Clara, CA, USA). Specifically, the microarray  (format 49-7875 with 11 µm 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.
Comment[SubmittedName]	Affymetrix Custom Array - NA-Staph-b520729F tiling microarray
Printing Protocol	http://www.affymetrix.com/technology/manufacturing/index.affx
Surface Type	unknown_surface_type
Surface Type Term Accession Number	#unknown_surface_type
Surface Type Term Source REF	The MGED Ontology
Substrate Type	unknown_substrate_type
Substrate Type Term Accession Number	unknown_substrate_type
Substrate Type Term Source REF	The MGED Ontology
Term Source Name	The MGED Ontology
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php[main]