The fidelity of L1000 depends on being able to quantify endogenous levels of intended landmark genes accurately and specifically. In synthesizing landmark gene-specific oligonucleotide probes we followed several computational procedures that maximized matches to the target DNA sequence while minimizing non-specific hybridization. However, as sequence-based QC methods are imperfect and measurement of a transcript might degrade in a multiplexed gene assay (e.g due to cross hybridization), we designed an experiment to empirically confirm probe performance.
