SINGLE-CELL CULTURE AND SEQUENCING WITH LIPID-MODIFIED OLIGOS
Researchers at UCSF have developed methods for sequencing a single cell from a cell culture sample and obtaining morphologic or phenotypic measurements and information by combining sequencing approaches and spatial hashing (e.g. barcoding) at a single cell level.
There exists a need in the state of the art for a method of obtaining morphological or phenotypic measurements and information linked with sequence information at the single-cell level. Current spatial transcriptomics technologies require dead tissues and are not compatible with live cell cultures. Current single-cell sequencing technologies do not include spatial indexes that allow users to map single-cell RNAseq data to cell morphology. Methods to integrate cell morphology and gene expression are limited by throughput and either require sacrificing detection efficiency and/or the number of genes probed.
Stage of Research
The inventors have developed methods for the high-throughput integration of single-cell long-term culture, imaging, and RNA-seq without the need for specialized substrates. The method utilizes lipid-modified oligonucleotides (LMO) to spatially label cultured single cells grown on any surface. The cells are resuspended into solution, for example by trypsinization, and then subjected to a standard single-cell sequencing platform. This invention enables imaging-based phenotypic observation on live cultured cells, which can be unambiguously linked with transcriptome information.
Applications
- Enabling the discovery of oncogenic cells based on imaging
- Enabling selection of engineered cells lines (e.g., CAR-T) that have desired cell-cell interaction properties; for example cells that kill cancer cells
- Sequencing cells with in-situ spatial hashing/barcoding
- High-throughput integration of single-cell morphology and transcriptome for individual neurons
- Paired spatial transcriptomics and force profiling for single cell analysis
- Integrating transcriptome and metabolome for pathway engineering of valuable metabolites
Advantages
- Compatibility with live cell cultures
- Inclusion of spatial indexes that allow users to map single-cell RNAseq data to cell morphology
- Compatibility with high-throughput methods
- Compatible with long-term cell culture and high resolution-imaging
- Single-cell precision
Stage of Development
Research – in vitro
Publications
WO2023/107598
Related Web Links
N/A
Keywords
Single cell, sequencing, lipid-modified, oligonucleotides
Technology Reference
CZB-216F; UCSF ref. no. SF2021-257