{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T11:13:27Z","timestamp":1790162007662,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,18]]},"group-title":"Bioengineering","reference-count":50,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"NIH","award":["R01DA059551"],"award-info":[{"award-number":["R01DA059551"]}]},{"name":"NIH","award":["U54 AI170856"],"award-info":[{"award-number":["U54 AI170856"]}]},{"name":"NIH","award":["R01AI150396"],"award-info":[{"award-number":["R01AI150396"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Many clinically important cell populations are defined by intracellular DNA or RNA signatures, but isolating and profiling these cells remains difficult. Probe-based in situ hybridization strategies that are compatible with cytometry have difficulty resolving low-abundance transcripts, integrated provirus, or single-copy genomic mutations. In contrast, droplet digital PCR achieves single-molecule sensitivity; however, subsequent cell isolation requires specialized microfluidic sorters that are slow and not widely available. Here, we introduce magniFIND-seq, a nucleic acid cytometry platform that combines the sensitivity of digital PCR with commercial magnetic-activated (MACS) and fluorescence-activated (FACS) sorting instruments. Single-cell genomes and transcriptomes are captured in agarose beads, target sequences are detected by digital PCR, and bead-bound amplicons are labeled with magnetic or fluorescent probes. Controlled evaporation shrinks beads from 55 to 20 \u00b5m, enabling scalable magnetic separation, fast single-bead FACS sorting, and their combination for high-purity recovery of rare populations. Using magniFIND-seq, we demonstrate multiplexed single-copy detection and FACS-based isolation of simian immunodeficiency virus proviral pol and env targets. Separately, using BCR::ABL1 as a disease-defining target, we enrich chronic myeloid leukemia cells and recover single-cell transcriptomes that resolve tyrosine kinase inhibitor-resistance programs. magniFIND-seq extends the throughput and accessibility of nucleic acid cytometry by engineering compatibility with commercial instruments.<\/jats:p>","DOI":"10.64898\/2026.09.12.751168","type":"posted-content","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T23:10:13Z","timestamp":1789773013000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-cell DNA cytometry with magnetic- and fluorescence-activated bead sorting"],"prefix":"10.64898","author":[{"given":"Seung Won","family":"Shin","sequence":"first","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sakshi","family":"Shah","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenchen","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atsuki","family":"Kawamura","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihui","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanrong","family":"Kang","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Klatt","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94609, 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