Samples of purified total RNA from six human cancer cell lines, purchased from Life Technologies, were subjected to L1000 profiling. L1000 expression profiles were generated for six cell lines in 3 independent LMA batches, each with 12 technical replicates, for a total of 216 total profiles (6 cell line × 12 replicates × 3 batches = 216). Within each cell line, we computed the Spearman correlation between all pairwise combinations of replicates (data level 3, see below), excluding the comparison of each replicate to itself. Three examples of paired comparisons and the full spectrum of correlations are shown in Figure S1C. We then computed the median correlation between each replicate and all others, yielding 36 values per cell line; and finally summarized using the median of medians so as to derive one value per cell line. These analyses showed that in general the L1000 assay has very high technical reproducibility.
