Faridani, O.R. et al. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.3701 (2016).

As the sequencing of single-cell transcriptomes takes off, many classes of RNA have been left behind. Nearly all protocols rely on poly-dT to prime the production of cDNA, which misses nonadenylated species, including microRNA (miRNA), small nucleolar RNA (snoRNA) and tRNA. A protocol from Faridani et al. addresses this gap by ligating 5' and 3' adaptors to all RNA species and suppressing amplification of the dominant rRNA fraction with masking oligos; unique barcodes also reduce amplification bias in this protocol. The researchers focused computational analysis on short species, finding thousands of miRNAs, tRNA fragments and snoRNA fragments, on average, in a single cell. They identified small RNAs that were differentially expressed between naive and primed human embryonic stem cells and showed that small RNA profiles can be used to distinguish between these cells types, HEK293FT and glioblastoma cells.