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

Patent Pending


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

Other Information


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

Categorized As