title: XC3 (TCR beta-based oligonucleotide microarray)
status: Public on Feb 13 2008
contact.city: Memphis
contact.first: Deanna
contact.middle: Cole
contact.last: Naeve
contact.email: deanna.naeve@stjude.org
contact.state: TN
contact.address: 332 N. Lauderdale
contact.department: Hartwell Center for Bioinformatics and Biotechnology
contact.country: USA
contact.institute: St. Jude Children's Research Hospital
contact.phone: 901-495-4847
organism: Homo sapiens
description: The Platform data table reflects a condensed representation of the multiply-printed oligos.
  The full array layout (GPL4259_complete_layout.txt) is linked as a supplementary file at the foot of this record.
manufacture_protocol: The array contains 27 TCR Vbeta probes and 13 Jbeta probes. The oligonucleotides are 50-62-mer sequences for Vbeta genes and 38-56-mer for Jbeta genes designed according to published sequences by using Vector NTI 9.0.0 software. The similarity of the probes was analyzed with Vector NTI 9.0.0 software. Oligonucleotides were synthesized by using phosphoramidite chemistry and were purified by using a cartridge system (Applied Biosystems, Foster City CA) in the Hartwell Center for Bioinformatics and Biotechnology Macromolecular synthesis lab at St Jude Children’s Research Hospital. Oligonucleotides were resuspended in 3xSSC to a concentration of 40µM and printed on poly-L-lysine-coated 1x3-inch glass slides by using an Omnigrid microarray printer (Genomic Solutions, Ann Arbor MI) with 16 CMP4 pins (Telechem, Sunnyvale CA) in the Functional Genomics lab of Hartwell Center. Each oligonucleotide was printed 48 times with 12 consecutive spots in each of 4 different semi-random areas across the array. After printing, slides were rehydrated, snap-dried and cross-linked by using a Stratalinker (Stratagene, La Jolla CA) and blocked with succinic anhydride.