A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell

Hiroko Matsunaga, Mari Goto, Koji Arikawa, Masataka Shirai, Hiroyuki Tsunoda, Huan Huang, Hideki Kambara*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called "bead-seq") to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes.

Original languageEnglish
Pages (from-to)9-16
Number of pages8
JournalAnalytical Biochemistry
Publication statusPublished - 2015 Feb 15
Externally publishedYes


  • Gene expression
  • Single cell
  • mRNA-seq

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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