Fig. 1

Identification and characterization of an intergenic lncRNA, LincIN. a Strategies for analyzing seven paired normal-tumor HEMC lines with high-density BeadChips (total 32 arrays) to identify differential expression in the intergenic lncRNA transcriptome. For each probe marker, the scanned raw signal intensities were processed by GenomeStudio software (Illumina, San Diego, CA, USA) to generate X and Y intensity values for allelic expression at each marker position. The total expression values for heterozygous markers were calculated using the sum of raw intensities from the X and Y channels. The total expression values for homozygous markers were assigned with either X or Y intensities based on the genotyping calls from corresponding gDNA signals. b The heatmap of top differentially expressed intergenic lncRNAs [FDR < 0.15, P < 0.005, |Log₂ of fold change (FC)| >1]. Highlighted probes (in bold) were mapped to the LincIN locus. c The physical map and genomic organization of LincIN were illustrated using the annotation tracks created by the UCSC Genome Browser. d Validation of LincIN expression in ten HMEC normal-tumor pairs by RT-qPCR (^* P < 0.05, t test; technical replicates: n = 4). e Rapid amplification of cDNA ends (RACE) analysis of LincIN transcripts resulted in two RNA variants (V1:1031 bp and V2: 837 bp) and full length (FL) of V1 was obtained by RT-PCR