title: Turkey skeletal muscle long oligonucleotide (TSKMLO) microarray
status: Public on Feb 01 2010
contact.city: East Lansing
contact.first: Kelly
contact.middle: R
contact.last: Sporer
contact.email: buckhamk@msu.edu
contact.state: MI
contact.address: 3365 Anthony Hall
contact.department: Food Science and Human Nutrition
contact.country: USA
contact.institute: Michigan State University
contact.phone: 517-355-8474
organism: Meleagris gallopavo
manufacture_protocol: Three skeletal muscle cDNA libraries from the developmental stages 18-day embryo, 1-day post-hatch chick, and 16-week market age bird were constructed and sequenced as in Reed et al. (2008).  Additional sequences for genes important in regulation of muscle growth, development, and extracellular matrix function were added.  Because alternative splicing has been identified as a potential mechanism in the differential regulation of the Ca2+ channel ryanodine receptor (RYR), possibly leading to downstream defects in postmortem meat quality (Chiang et al. 2004; Chiang et al. 2007), oligos were also designed to represent five different alternatively spliced products of RYR.  In total, 5809 70-mer oligonucleotides were commercially designed (Invitrogen, Carlsbad, CA).  A unique set of control probes were designed for thirty randomly chosen genes with the stipulation that the gene be greater than 1500 bases in length.  These controls consisted of: one scrambled sequence control, three “distance” controls that included oligos designed within 500, 501-1000, and 1001-1500 bases from the 3’ of the sequence, and six “mismatch” controls including 3, 5, 10, 15, 20, or 25 mismatched bases, totaling 300 control probes.
  The 384 well print plates were prepared by diluting the probes in print buffer (3X SSC, 0.005% SDS) to a final concentration of 60uM. The arrays were printed on Corning UltraGAPS slides using a Genomic Solutions (GeneMachines) Omnigrid 100 spotting robot using Telechem Chipmaker 3 pins. The arrays consist of 48 subarrays (in a 4 by 12 pattern) each having a 16 by 16 grid of probe spots. Spot spacing is 250um on center and subarray (ie. pin) spacing is 4500um.  Probes were spotted in duplicate, and “blank” spots (spotting solution only) were included in each patch of the microarray.