TY  - JOUR
TI  - Identification of DNA-Binding Factor Enrichment in Chromatin Accessibility Data to Define a Persister Cell Signature
AU  - Ajay, Vidya 
AU  - Dumbrava, Mihai G.
AU  - Gaspar-Maia, Alexandre 
AU  - Ismail, Wazim Mohammed
VL  - 16
IS  - 16
PY  - 2026
DA  - 2026/08/20
SP  - e5800
C1  - Bio-protocol 2026;16:e5800
DO  - 10.21769/BioProtoc.5800
UR  - https://doi.org/10.21769/BioProtoc.5800
AB  - Chemotherapy-resistant persister cells are a major driver of cancer recurrence, yet their epigenetic basis remains poorly characterized. This protocol describes a computational pipeline for identifying DNA-binding factors (DBFs) that are enriched in accessible chromatin that collectively define a persister cell signature (PCS). Starting from single-nucleus ATAC-seq (snATAC-seq) data processed through the 10x Genomics CellRanger ARC pipeline, this protocol covers (1) the creation of a Seurat/Signac object with ATAC peaks, (2) the optional integration of DNA-binding data from the ReMap2022 database as a per-cell chromatin module assay, (3) differential accessibility analysis across clinically defined comparison groups, and (4) identifying and defining the top enriched DBFs as the PCS. This approach is applicable to any snATAC-seq dataset in which cells can be grouped by clinical response, treatment status, or resistance phenotype.
KW  - Chromatin accessibility, Multiome, snATAC-seq, ChIP-seq, CUT&amp
KW  - RUN, Single cell, Epigenomics
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False