To detect gene-specific sequences, Luminex beads were coupled to DNA barcodes complementary to each barcode used in our collection of probes. Because Luminex produces 500 distinct bead colors and the L1000 set consists of 978 genes, 2 barcodes were coupled to beads of each color (see below); this was done in separate batches - one barcode per batch - and then the pairs were mixed in a 2:1 ratio prior to use. Luminex magnetic beads were added in 500 μl aliquots to each well of 96 deep-well plates. Beads were pelleted and resuspended in 62.5 μl binding buffer (0.1 M 2- [N-morpholino]ethanesulfonic acid; pH 4.5), to which was added 100 pmol capture barcode. 6.25 μl of freshly prepared 10 mg/ml aqueous solution of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (Pierce, Milwaukee, WI, USA) was added to each well followed by incubation at room temperature in the dark for 30 minutes. This step was repeated and then 180 μl 0.02% Tween-20 was added. Beads were pelleted and washed in 0.1% SDS in TE, pH 8.0 buffer. Beads were stored in TE in the dark
