title: DASL Human 1.5K Cancer Panel
status: Public on Jan 30 2009
contact.city: Brisbane
contact.first: Leonard
contact.last: Da Silva
contact.email: l.dasilva@uq.edu.au
contact.address: Herston Road
contact.country: Australia
contact.institute: University of Queensland
contact.phone: +61733466106
organism: Homo sapiens
manufacture_protocol: The cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) Assay is designed for RNA profiling of up to 1,536 targets using partially degraded RNA as found in formalin-fixed, paraffin-embedded samples.
  The core of the experiment relies on beadarray technology - Illumina’s BeadArray Technology is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in one of Illumina’s assays. Because the beads are positioned randomly, a decoding process is carried out to determine the location and identity of each bead in every array location. Decoding is an automated part of array manufacture - extracted from www.illumina.com.
  Assay Probe Design: As described by Bibikova et al Am J Pathol. 2004 November; 165(5): 1799–1807  - "Two probe oligonucleotides are designed to interrogate each target site on the cDNA, with 3 to 10 target sites per gene (average 6 sites). The first oligo consists of two parts: the gene-specific sequence and a universal PCR primer sequence (P1, 5′-ACTTCGTCAGTAACGGAC-3′) at the 5′-end. The second oligo consists of three parts: the gene-specific sequence, a unique address sequence which is complementary to one of 1520 capture sequences on the array, and a universal PCR primer sequence (P2, 5′-GTCTGCCTATAGTGAGTC-3′) at the 3′-end. A single address sequence is uniquely associated with a single target site. This address sequence allows the PCR-amplified products to hybridize to a universal microarray bearing the complementary probe sequences. The gene-specific sequence is designed with Tm ranging from 57°C to 62°C."