­HYDROGEL PURIFICATION OF CELL MATERIALS FOR PCR-ACTIVATED CELL SORTING

­HYDROGEL PURIFICATION OF CELL MATERIALS FOR PCR-ACTIVATED CELL SORTING

Researchers at the NIH and UCSF have developed methods that detect RNA or DNA markers with single molecule sensitivity in cells of interest that allow rapid isolation of these cells or extracts/derivatives of these cells for in-depth transcriptomic, genomic or epigenomic analyses.

Single-cell genomic, epigenomic and transcriptomic technologies can identify unique cell subsets with important physiologic roles, but these ‘omic’ signatures cannot always be linked to unique surface markers, hampering their re-isolation for in-depth analyses. Moreover, many single-cell methods require sequencing large numbers of cells and are therefore poorly suited to characterize rare cell subsets. Finally, PCR-activated cell sorting technologies do not permit sensitive sequencing of recovered cells. Therefore, there exists a need in the art for high-throughput cytometry methods that detect RNA or DNA markers with single molecule sensitivity in cells of interest that allow rapid isolation of these cells or extracts/derivatives.

Stage of Research

The inventors have developed a method called FIND-seq; a high-throughput method to isolate and sequence rare cells defined by nucleic acid markers. FIND-seq is a unique tool for the investigation of cell subsets identified in single-cell genomic studies because it can directly target the nucleic acid markers that define them.

Applications

• Cell sorting based on RNA or DNA markers
• High throughput microfluidic capture of cell genomes and transcriptomes in agarose beads
• Sorting and sequencing of single cells based on single-copy DNA markers
• Whole transcriptome sequencing of HIV DNA+ cells by HIV-FIND-seq

Advantages

• Process millions of cells with single molecule detection sensitivity and produce high quality transcriptome data.
• Eliminate the need to analyze large numbers of unrelated cells when studying small cell populations.
• Flexible processing of cellular material in porous, biocompatible and thermally reversible hydrogels makes the method well suited for additional multi-omic readouts including genomic, epigenomic or proteomic measurements.
• Can accelerate the study of cells for which transgenic animals or antibodies are unavailable because FIND-seq can sort cells based on genomic DNA or RNA markers.

Stage of Development

Research – in vitro

Keywords

Single cell transcriptomics, high-throughput, single cell genomics, hydrogel, microfluidic

Technology Reference

CZ Biohub SF ref.no. CZB-271F

UCSF ref. no. SF2023-081