FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics.

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Traditional cell isolation relies on surface protein markers, limiting the study of rare cell subsets.
• Genomic and transcriptomic data increasingly define cell subsets computationally.
• Nucleic acid-based isolation complements existing methods, enabling access to rare and unique cell populations.

Purpose of the Study:

• To detail the protocol for Focused Interrogation of Cells by Nucleic Acid Detection and Sequencing (FIND-seq).
• To present protocol updates for detecting and sequencing rare HIV-infected cells with intact viral genomes.
• To enable mechanistic studies of rare cell subsets previously difficult to isolate and sequence.

Main Methods:

• Development and application of the FIND-seq nucleic acid cytometry platform.
• Utilizing RNA or DNA markers for rare cell isolation.
• Performing bulk or single-cell transcriptomic analysis post-isolation.
• Protocol updates for detecting and sequencing rare HIV-infected cells harboring intact viral genomes.

Main Results:

• FIND-seq successfully isolates rare cells based on nucleic acid sequences.
• The platform has been previously applied to study XBP1 splicing in astrocytes and HIV persistence in CD4 T cells.
• Updated FIND-seq protocol allows whole transcriptome sequencing of rare HIV+ cells with intact viral genomes.

Conclusions:

• FIND-seq provides a powerful method for isolating and studying rare cell subsets defined by nucleic acid sequences.
• The detailed protocol and updates facilitate research on previously inaccessible cell populations.
• This technology is expected to advance mechanistic studies of rare cells, including those relevant to HIV persistence.