Fig. 8
Validation of PLAIDOH’s functional predictions for a lncRNA highly expressed in human NHL. a UCSC Genome browser view of HK4me3 ChIP-seq (NHL) and RNA-seq (NHL, normal B cells) for the RP11-960 L18.1 locus. b XY plot shows Enhancer versus LncRNA Transcript Cis-regulatory Scores in primary NHL samples, highlighted are RP11-960 L18.1 and the two most proximal coding genes. c Expression of PLCG2 and RP11-960 L18.1 measured by qRT-PCR in HBL1 lymphoma B cell line treated with scramble or one of two RP11-960 L18.1 shRNAs. d Western Blot for PLCG2 or GAPDH in HBL1 cells treated with scramble or one of two RP11-960 L18.1 shRNAs. Triangles indicate relative number of cells loaded on the gel. e Subcellular localization of RNA transcripts determined by cell-fractionation of control (WT) HBL1 cells followed by qRT-PCR (CP: cytoplasm, NC: nuclear, NP: nucleoplasm, CA: chromatin-associated). f Plot shows lncRNA expression versus log10 RBP binding-site density per kilobase of RNA transcript for each lncRNA/RBP interaction, highlighted are RBPs that bind RP11-960 L18.1. Data point size is scaled to RBP expression level and subcellular localization interactions are colored as in Fig. 7