Protocol to maximize single-nuclei multiome library complexity for limited primary tissues via optimized sample preparation and library synthesis
| Title | Protocol to maximize single-nuclei multiome library complexity for limited primary tissues via optimized sample preparation and library synthesis |
| Publication Type | Journal Article |
| Year of Publication | 2026 |
| Authors | Uddin F, Pandit A, Kudpaje A, Notani D, Sabarinathan R |
| Journal | STAR Protocols |
| Volume | 7 |
| Pagination | 104640 |
| ISSN | 2666-1667 |
| Keywords | Cancer, Gene Expression, Genomics, molecular biology |
| Abstract | Summary 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. |
| URL | https://www.sciencedirect.com/science/article/pii/S2666166726002935 |
| DOI | 10.1016/j.xpro.2026.104640 |