Transcriptional profiling of cells sorted by RNA abundance

Sandy Klemm, Stefan Semrau, Kay Wiebrands, Dylan Mooijman, Dina A Faddah, Rudolf Jaenisch, Alexander van Oudenaarden

Research output: Contribution to journal/periodicalArticleScientificpeer-review

27 Citations (Scopus)


We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.

Original languageEnglish
Pages (from-to)549-51
Number of pages3
JournalNature Methods
Issue number5
Publication statusPublished - May 2014


  • Alleles
  • Animals
  • Cell Culture Techniques
  • Cellular Reprogramming
  • Doxycycline
  • Embryonic Stem Cells
  • Fibroblasts
  • Flow Cytometry
  • Gene Expression Profiling
  • Genome-Wide Association Study
  • Green Fluorescent Proteins
  • In Situ Hybridization, Fluorescence
  • Induced Pluripotent Stem Cells
  • Mice
  • NIH 3T3 Cells
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • RNA
  • RNA, Messenger
  • Transcription, Genetic
  • Transgenes


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