A-AFFY-48 - Affymetrix Custom Array - RMLchip [RML-chipa510998]

Borrelia burgdorferi;Chlamydia trachomatis;Coxiella burnetii;Staphylococcus aureus;Streptococcus pyogenes;Yersinia pestis;Yersinia pseudotuberculosis
The RMLchip is an anti-sense oligonucleotide expression array (18 mm feature size), containing 21 genomes from 6 different genus', consisting of ~249,690 25-mer probe pairs, with each C. burnetii ORF represented by 16 probe pairs that consist of a perfect-match (PM) probe and a mismatch (MM) probe. The MM probe has a single substitution at position 13 relative to the PM probe. All probe sequences were pruned against chip-containing genomes, human, rat, mouse genomes and 12 additional genome sequences of known human commensals. Pruning was performed in order to exclude sequences that might cross-hybridize with sequences on the chip, commensals and host DNA. The C. burnetii component of the RMLchip consists of probe sets specific to 2024 full length genomic ORFs (1988 chromosomal ORFs and 36 plasmid ORFs) of the sequenced Nine Mile isolate (RSA493) (Seshadri et al. 2003). Probe sets specific for 79 disrupted ORFs that contain deletions or point mutations, resulting in premature stop codons or frameshifts, were also included. Probe sets specific for one representative of the 21 IS1111A, 5 IS30 and 3 ISAs1 IS element families were also included. The total coding region of the C. burnetii genome is 1,705,446 base pairs (bps). The probe sets on the RMLchip emcompass approximately 30% (511,725 bps) of this region.
Affymetrix, Inc. (support@affymetrix.com);Paul Beare (pbeare@niaid.nih.gov)
Experiment E-TABM-35
Array DesignA-AFFY-48.adf.txt