miR-140-3p isomiRs are abundantly expressed in cartilage. (A) Pie chart illustrating the relative abundance of all miRNAs expressed in cartilage, data combines isomiR and canonical reads for each miRNA. (B) Pie chart illustrating the isomiR type for all reads aligned to miR-140-3p. (C) Pie chart illustrating seed sequences for all reads aligned to miR-140-3p, >99% of reads have one of two seed sequences; ACCACAG (blue) and CCACAGG (red). (D) Pie chart of the percentage of templated and nontemplated reads for miR-140-3p within cartilage. (E) Histogram of all sequencing reads aligned to miR-140-3p in cartilage. (F) Histogram of sequencing reads aligned to miR-140-3p, whose 5′ end is as indicated in miRBase. (G) Histogram of sequencing reads aligned to miR-140-3p, whose 5′ end is one nucleotide shorter than indicated in miRBase. (H) Bar chart indicting the sequences and number of reads that contribute to each of the two seed sequences. Individual bars represent total read number from three separate individuals. (I) qRT-PCR for miR-140-3p.1 and miR-140-3p.2. Assays designed to detect each isomiR are able to distinguish between miR-140-3p.1 and miR-140-3p.2 spike-ins (twofold serial dilution) and detect high expression of each isomiR in cartilage (twofold serial dilution).
