title: Agilent-016097 UNIFE_HGDMDAntisense_44K_V1.0
status: Public on Jun 05 2011
contact.city: Ferrara
contact.first: Matteo
contact.last: Bovolenta
contact.email: bvlmtt@unife.it
contact.address: 74, Fossato di Mortara
contact.department: Life Sciences and Biotechnology
contact.country: Italy
contact.institute: University of Ferrara
contact.phone: 00390532974485
organism: Homo sapiens
description: We tiled the entire DMD gene, in both sense and antisense directions, using the web-based Agilent eArray database, Version 4.5 (Agilent Technologies), with 60-mer oligos every 66 bp of repeat-masked genome sequence. We defined probe sets for both orientations, encompassing the DMD exons, promoters, introns, predicted MiRNA (identified by PromiRII) and conserved non-coding sequences (CNSs) identified within dystrophin introns using the VISTA programme (http://genome.lbl.gov/vista/index.shtml). Two specific sets of probes were designed to cover, in both directions, the cDNA sequences of a group of control genes (Supplementary Table S1) identified in the Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/) and expressed equally in both normal and dystrophic muscles. Each probe set was opportunely distributed and replicated several times in order to obtain two 4x44k microarrays, referred to as DMD GEx Sense and DMD GEx Antisense, respectively, able to detect transcripts in the same and opposite directions as that of DMD gene transcription.
manufacture_protocol: see manufacturer's web site at http://www.agilent.com/