Protocol to maximize single-nuclei multiome library complexity for limited primary tissues via optimized sample preparation and library synthesis.

Authors

Faizan Uddin, Awadhesh Pandit, Akshay Kudpaje, Dimple Notani, Radhakrishnan Sabarinathan

Published in

STAR protocols. Volume 7. Issue 3. Pages 104640. Jun 19, 2026. Epub Jun 19, 2026.

Abstract

Single-nuclei multiomic profiling of clinical biopsies is often hindered by limited tumor mass and high debris content. Here, we present a protocol for the dissociation of head and neck squamous cell carcinoma (HNSCC) and matched-normal tissues using a mechanical-enzymatic workflow. We describe steps for minimizing ambient nucleic acid background by red blood cell (RBC) lysis and DNase-I treatment and for removing cellular debris using density gradient centrifugation. We then detail procedures for isolating intact nuclei and modified single-nuclei assay for transposase-accessible chromatin sequencing (sn-ATAC) and 3'-GEX (gene expression) indexing PCR and size selection to maximize library complexity.

PMID:
42319832
Bibliographic data and abstract were imported from PubMed on 20 Jun 2026.

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