Smart-Seq2

Overview

Smart-Seq2 is a plate-based, full-length single-cell (or single-nucleus) RNA sequencing protocol that uses template-switching reverse transcription with locking oligonucleotides to capture transcripts from 5’ to 3’. Unlike droplet-based UMI methods, Smart-Seq2 provides high-depth, full-length coverage per cell, enabling detection of splice isoforms and improving coverage of lowly expressed genes, at the cost of lower cell throughput.

Used by

  • PMID:27806376 — plate-based Smart-Seq2 scRNA-seq applied to 4,347 FACS-sorted live single cells (calcein AM+/TO-PRO-3−) from 6 untreated IDH-mutant 1p/19q co-deleted oligodendrogliomas; 96 cells from MGH60 were also profiled in parallel with a UMI-based protocol with concordant results, validating Smart-Seq2 accuracy in the tumor context PMID:27806376.
  • PMID:34493726 — Smart-Seq2 nuc-Seq applied to 11 neuroblastoma tumors (4,224 nuclei; average 709,676 reads/nucleus), 3 postnatal human adrenal glands (1,536 nuclei; ~485,000 reads/nucleus), and 5 mouse adrenal glands (1,920 cells; ~670,000 reads/cell); the full-length protocol supported identification of a novel NTRK2+/CLDN11+ cholinergic progenitor population absent from mouse adrenal gland PMID:34493726.
  • PMID:39975212 — G&T-Seq + Smart-Seq2 used for matched DNA/RNA profiling of 297 clonally expanded single melanocytes from 58 skin biopsies; colonies of ~230 cells underwent joint DNA amplification and Smart-Seq2 RNA sequencing; gene expression used to define HighMut (pigmentation/differentiation) and LowMut (neural-crest/stem-like) melanocyte transcriptional states; reads aligned with STAR v2.1.0 PMID:39975212.

Notes

  • Smart-Seq2 depth is higher than droplet methods per cell but total cell numbers are modest; rare subpopulations could be missed compared with 10x Chromium-scale datasets PMID:34493726.
  • Full-length coverage enables detection of allele-specific expression and splice variants that UMI-based 3’-end protocols cannot resolve PMID:27806376.
  • Corpus-grown slug; not present in canonical ontology.

Sources

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