Single-cell profiling of total RNA using Smart-seq-total

The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current RNA-seq methods are unable to simultaneously monitor both short and long, poly(A)+ and poly(A)- transcripts at the single-cell level, and thus deliver only a partial snapshot of the cellular RNAome.

Stanford University researchers have developed Smart-seq-total, a method capable of assaying a broad spectrum of coding and non-coding RNA from a single cell. Built upon the template-switch mechanism, Smart-seq-total bears the key feature of its predecessor, Smart-seq2, namely, the ability to capture full-length transcripts with high yield and quality. It also outperforms current poly(A)- independent total RNA-seq protocols by capturing transcripts of a broad size range, thus, allowing us to simultaneously analyze protein-coding, long non-coding, microRNA and other non-coding RNA transcripts from single cells. The researchers used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T and MCF7 cells as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. The researchers show that simultaneous measurement of non-coding RNA and mRNA from the same cell enables elucidation of new roles of non-coding RNA throughout essential processes such as cell cycle or lineage commitment. Moreover, they show that cell types can be distinguished based on the abundance of non-coding transcripts alone.

Schematic comparison of Smart-seq2 and Smart-seq-total pipelines


Following cell lysis, total cellular RNA is polyadenylated, primed with anchored oligodT and reverse transcribed in a presence of the custom degradable TSO. After reverse transcription, TSO is enzymatically cleaved, single-stranded cDNA is amplified and cleaned up. Amplified cDNA is then indexed, pooled and depleted from ribosomal sequences using DASH33. Resulting indexed libraries are then pooled and sequenced on Illumina platform.

Isakova A, Neff N, Quake S. (2020) Single cell profiling of total RNA using Smart-seq-total. bioRXiv [preprint]. [abstract]

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