Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

Dongju Shin, Wookjae Lee, Ji Hyun Lee, Duhee Bang

Research output: Contribution to journalArticle

7 Citations (Scopus)


The development of high-throughput single-cell RNA sequencing (scRNA-seq) has enabled access to information about gene expression in individual cells and insights into new biological areas. Although the interest in scRNA-seq has rapidly grown in recent years, the existing methods are plagued by many challenges when performing scRNA-seq on multiple samples. To simultaneously analyze multiple samples with scRNA-seq, we developed a universal sample barcoding method through transient transfection with short barcode oligonucleotides. By conducting a species-mixing experiment, we have validated the accuracy of our method and confirmed the ability to identify multiplets and negatives. Samples from a 48-plex drug treatment experiment were pooled and analyzed by a single run of Drop-Seq. This revealed unique transcriptome responses for each drug and target-specific gene expression signatures at the single-cell level. Our cost-effective method is widely applicable for the single-cell profiling of multiple experimental conditions, enabling the widespread adoption of scRNA-seq for various applications.

Original languageEnglish
Article numbereaav2249
JournalScience Advances
Issue number5
Publication statusPublished - 2019 May 15


All Science Journal Classification (ASJC) codes

  • General
  • Physics and Astronomy (miscellaneous)

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