Figure 5. Characterization of top validated candidate lncRNAs.

(A) Summary qPCR data shown as log2 fold change expression relative to Renilla Luciferase knockdown. Average values shown as a heatmap from three biological replicates (independent dox inductions) and two independent clonal cell lines. Relative expression was calculated as delta delta Cq using Gapdh as reference. For each lncRNA knockdown (rows), relative expression for the lncRNA itself, and its upstream and downstream genes are shown (columns). (B) Enrichment for Macrophage Differentiation (Ingenuity Pathway Analysis gene set) and Leukemia Stem cell Signature (Krivtsov et al., 2006) gene sets upon lncRNA knockdown was performed using Gene Set Enrichment Analysis. (C) Flow cytometry analysis of cKit and CD11b (Mac-1) surface markers upon lncRNA or Renilla knockdown. A representative plot per lncRNA is shown on the left. Geometric Mean fold change relative to Renilla knockdown is shown as the average of four biological replicates. Error bars represent s.e.m.

Figure 5—figure supplement 1. Validated lncRNA hits are not generally required for proliferation.

Representative proliferation assays bar plots for AML and breast cancer cell lines (left). Heat map representing normalized depletion by day 14 after infection for the nine lncRNAs that were further analyzed (right).