RNA-seq data Mapping with Tophat/Bowtie Assembling by Cufflinks without -G option Detect differentially expressed bins Putative differentiall y expressed lincRNA UCSC database (affyU133Pl us2, knownGene) Count reads on 200bp bins Select putative transcripts sharing genomic position Get intergenic transcripts (Exclusive) RNA-seq data Mapping with Tophat/Bowtie Get lincRNA probe list (Exclusive) Detect differentially expressed lincRNA Query lincRNA expression value UCSC database (affyU133Plu s2, knownGene) Affymetrix microarray data (GENT database) Run Cufflinks with -G option (affyU133Plus. gtf from UCSC) Detect differentially expressed lincRNA Intersection by probe ID Putative differentia lly expressed lincRNA B A Supplementary Fig 1.