title: 100319_HG19_Immunity_JD_CGH Array
status: Public on Nov 19 2013
contact.city: Tallahassee
contact.first: Jonathan
contact.middle: Hancock
contact.last: Dennis
contact.email: dennis@bio.fsu.edu
contact.state: FL
contact.address: 319 Stadium Dr.
contact.department: Biological Science
contact.country: USA
contact.institute: The Florida State University
contact.phone: 850-645-9274
organism: Homo sapiens
description: designname=100319_HG19_Immunity_JD_CGH  designid=11672
  We used a custom-designed high-resolution DNA microarray that covers 2 kb flanking the TSS 472 immunity- and inflammation-related genes.  Only unique probes were printed on the microarray, and repeats were masked around the TSS.  Both forward and reverse DNA strands were printed on the microarray.  The 60-mer oligonucleotide probes were tiled with an average 47-bp overlap.  We used NimbleGen’s 12-plex and HD2 design for our microarrays.  Each locus on the microarray contains approximately 180 probes of a median spacing of 12.5 bps.  Samples were labeled (nucleosomally protected DNA Cy3 and genomic DNA Cy5) and hybridized to the custom tiling microarray (Roche) according to manufacturer’s instructions.
manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html