title: HGU-MRC-Bickmore Mouse Hoxb/d 22K tiling v1.0
status: Public on Mar 04 2010
contact.city: Edinburgh
contact.first: Graeme
contact.middle: Richard
contact.last: Grimes
contact.email: graeme.grimes@ed.ac.uk
contact.address: Western General Hospital, Crewe Road
contact.department: Human Genetics Unit
contact.country: United Kingdom
contact.institute: University of Edinburgh, The Institute of Genetics and Cancer
organism: Mus musculus
description: Tiling path array of oligos on HoxB and HoxD clusters :1 oligo / 250 bp in the core region containing the Hox genes,1 oligo / 500 bp in the flanking regions,1 oligo / 50kb outside flanking regions.These tiling oligos are designed alternatively on each strand. The position number (NCBI built m35) in the files is the 5’ base for the forward oligos and the 3’ for the reverse oligos (so one given oligo and the corresponding reverse oligo have the same position number). Other regions on the array are:Oct4  exons, promoter, flanking regions with low resolution,Sox2 exons, promoter, flanking regions with low resolution, Nanog  exons, promoter. Control genes for array are; Ncl : exons, promoter, flanking regions with low resolution, RPL19  exons, Rrm2 exons, HPRT exons, promoter, c-myc, exons and other regions contains MAR and CTCF binding sites, Hbb-b1 exons and regulatory elements, Cdkn1a exons, promoter and regulatory elements, Oprk1 exons and regulatory elements and  Mouse major and minor satellite DNA. Mismatch control oligos are the same as the oligos in exons but containing 1, 3, 5,7 ,10 mismatches. (NB : the Ncl mismatch oligos have been designed on the wrong strand). Other control probes are NM_000015.1 and Drosophila sequences.
manufacture_protocol: Amine-modified oligos were spotted at 20uM in 1 x Nexterion Spot buffer containing 0.005% triton X100 onto Codelink activated slides