Fig. 1

Defining the lncRNA transcriptome of human primary granulocytes. a Sample processing overview. b LncRNA identification overview. Granulocyte PolyA+ RNA-seq data from 10 donors was used for transcriptome assembly and filtered to create an annotation with 1,591 lncRNA loci containing 6,249 lncRNA transcripts (Additional file 1: Figures S1-3). c Positional classification of lncRNA loci relative to the nearest protein-coding gene. Twenty-five percent (402) are bidirectional (light gray), 33 % (530) are antisense (medium gray), and 42 % (659) are intergenic (dark gray). Positional classes are illustrated underneath (blue: protein-coding gene, green: lncRNA). d Example of a novel granulocyte antisense lncRNA locus. Top: 3' part of AJAP1 protein-coding gene (blue) and the novel antisense gra1110 lncRNA locus (green). Underneath: normalized to read number RNA-seq signal from sample D2-2_pa_100ss (Additional file 2B); GENCODE-v19 protein-coding genes (blue lines) and de novo annotated mRNAs (blue) and lncRNAs (green) showing lncRNA transcripts in locus gra1110 (Additional files 3, 4, and 6). e Overlap of granulocyte de novo lncRNA annotations (green) with commonly used public lncRNA annotations (gray) (RefSeq: 8,236 lncRNA transcripts, GENCODE-v19: 23,898 lncRNA transcripts, Cabili [14]: 21,630 lncRNA transcripts) and the ‘MiTranscriptome’ annotation (brown) [29]. f Validation of granulocyte de novo lncRNAs by cloning. Three de novo lncRNA loci (84, 152, 187) are shown (see also Additional file 1: Figures S4-S8). Top to bottom for each: scale and chromosome, de novo lncRNA transcript annotation in each locus (green isoforms), cloning result (black lines) showing BLAT alignment of the Sanger sequenced cloned cDNA