Intracellular DNA Barcoding Method for Single-Cell Amplification and Sequencing

Studying single cells is difficult due to the laborious and costly cell isolation procedures which restrict throughput and impede the analysis of large numbers of cells or multiple samples in a single experiment. ASU researchers previously developed a method which used the cell’s membrane as a container for different reactions. One such reaction was amplifying a cell's DNA in situ to enable in situ single-cell downstream DNA sequencing. This can be useful for many reasons, however, there is a need to process cells from numerous samples and later de-multiplex them computationally so as to track which sequenced DNA came from which cell. To do this, cell-specific barcodes have to be appended to the amplified DNA. Since the amplified DNA is double stranded, this is incompatible with other approaches such as the one currently used to append barcodes to RNA or to RNA-cDNA hybrids.

 

Researchers at the Biodesign Institute of Arizona State University have developed a novel method enabling effective barcoding of intracellularly amplified double-stranded DNA for scalable single-cell DNA sequencing. This innovative method leverages the cell membrane as a natural container for intracellular reactions, allowing for amplification of a cell's DNA in situ and appending unique cell-specific barcodes onto the amplified double-stranded DNA.

 

Unlike existing methods that barcode RNA or RNA-cDNA hybrids, this approach uniquely enables barcoding of DNA within the cell, overcoming previous incompatibilities and enabling detailed downstream DNA sequencing and analysis at the single-cell level.

 

Potential Applications

Benefits and Advantages

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