Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

Nat Commun. 2016 Jul 8:7:12139. doi: 10.1038/ncomms12139.


Laser capture microscopy (LCM) coupled with global transcriptome profiling could enable precise analyses of cell populations without the need for tissue dissociation, but has so far required relatively large numbers of cells. Here we report a robust and highly efficient strategy for LCM coupled with full-length mRNA-sequencing (LCM-seq) developed for single-cell transcriptomics. Fixed cells are subjected to direct lysis without RNA extraction, which both simplifies the experimental procedures as well as lowers technical noise. We apply LCM-seq on neurons isolated from mouse tissues, human post-mortem tissues, and illustrate its utility down to single captured cells. Importantly, we demonstrate that LCM-seq can provide biological insight on highly similar neuronal populations, including motor neurons isolated from different levels of the mouse spinal cord, as well as human midbrain dopamine neurons of the substantia nigra compacta and the ventral tegmental area.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Animals
  • Dopaminergic Neurons / metabolism
  • Female
  • Gene Expression / physiology
  • Gene Expression Profiling / methods*
  • Humans
  • Laser Capture Microdissection / methods*
  • Male
  • Mesencephalon / cytology
  • Mesencephalon / metabolism
  • Mice
  • Microscopy / methods*
  • Models, Animal
  • Motor Neurons / metabolism
  • Mouse Embryonic Stem Cells
  • Pars Compacta / metabolism
  • Poly A / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / isolation & purification
  • Sequence Analysis, RNA / methods*
  • Spinal Cord / cytology
  • Ventral Tegmental Area / metabolism


  • RNA, Messenger
  • Poly A