Lipid-Modified Oligonucleotides For Sample Barcoding in Droplet Microfluidics-Based Single-Cell RNA Sequencing

Tech ID: 29668 / UC Case 2018-119-0

Invention Novelty

A new strategy for barcoding single living cells using lipid-modified oligonucleotides that can vastly enhance sample multiplexing in droplet microfluidics-based RNA sequencing

Value Proposition

Single-cell RNA sequencing has recently emerged as a powerful tool for mapping transcriptional changes in heterogeneous cell populations. Recently, large-scale genomic screens combined with single-cell RNA sequencing have been utilized to understand complex biological phenomena. Novel insights could also be gained from coupling single-cell RNA sequencing to chemical library or drug screens, but methods for stably labeling living cells with oligonucleotide barcodes are lacking. Lipid-modified oligonucleotides represent an inexpensive, scalable, and technically simple method for labeling cell membranes in a fashion that interfaces with existing single-cell RNA sequencing workflows using droplet microfluidics.

This new cell barcoding method provides the following advantages:

  • Significantly increase the current sample and cell multiplexing capacity of scRNA sequencing workflows.
  • Dramatically decrease labor and material costs and increase efficiency of creating a sequencing library by performing the multiplexing early in the workflow
  • Avoid or remove technical artifacts due to fixation, doublets, or activation of cell surface receptor-mediated transcriptional responses
  • Uses a universal cell-labeling platform that can be applied in any biological context, without requiring a priori knowledge of cell surface markers
  • Barcodes are inexpensive to synthesize and stable at room temperature.

Technology Description

Researchers at University of California, San Francisco have developed a new cell barcoding method that uses lipid-conjugated oligonucleotides to efficiently label single live cells derived from distinct patients or test conditions. Oligonucleotide barcodes (engineered with a PCR handle, unique identifier and PolyA sequence) can be subsequently introduced to the cells and subsets of the cells processed for droplet microfluidics-based RNA sequencing library preparation. This method can be commercially applied in the form of 96-, 384-, 1536- or 3456-well plates containing lipid-modified oligonucleotides pre­hybridized to sample barcodes. Cells derived from distinct perturbations or clinical samples could be barcoded via dispensing into unique wells upstream of labeling and single-cell RNA sequencing.

Looking for Partners

To develop and commercialize this technology, potentially as a cell barcoding kit for droplet microfluidics-based RNA sequencing.


Single cell RNA sequencing library preparation

Stage of Development

Proof of Concept

Data Availability


Patent Status

Country Type Number Dated Case
European Patent Office Published Application 3818151 05/12/2021 2018-119
China Published Application CN112654699A 04/13/2021 2018-119

Additional Patents Pending


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  • Chow, Eric D.
  • Gartner, Zev J.
  • McGinnis, Christopher S.
  • Patterson, David M.
  • Weber, Robert J.

Other Information


Single Cell RNA Sequencing, Barcoding, Droplet microfluidics, Library preparation, Clinical & preclinical samples

Categorized As

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