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Peer-reviewedCC BYSTAR protocols

Protocol for profiling chromatin accessibility in human small-cell lung cancer FFPE-derived samples using Omni-ATAC-seq

  • Eralda Salataj1
  • Kenta Kawasaki2
  • Joan Massagué3
  • Charles M. Rudin4
  • Iestyn Whitehouse1
  • Richard Koche1
  • Pierre-Jacques Hamard1
4 affiliations
  1. 1Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
  2. 2Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
  3. 3Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
  4. 4Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Abstract

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) on formalin-fixed paraffin-embedded (FFPE) samples maps accessible chromatin in archival tissues, but DNA degradation and crosslinking remain significant challenges when processing these samples. Here, we present a protocol for Omni-ATAC-seq on degraded human small-cell lung cancer (SCLC) FFPE-derived samples. We detail steps for successful nuclei isolation, efficient tagmentation, and optimal library amplification to overcome the low signal-to-noise ratio. This protocol enables high-quality epigenetic profiling, turning archived SCLC samples into valuable resources for studying disease progression.

For complete details on the use and execution of this protocol, please refer to Kawasaki et al.1

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Cite

BibTeXRIS
BibTeX
@article{salataj2026protocol,
  title = {{Protocol for profiling chromatin accessibility in human small-cell lung cancer FFPE-derived samples using Omni-ATAC-seq}},
  author = {Eralda Salataj and Kenta Kawasaki and Joan Massagué and Charles M. Rudin and Iestyn Whitehouse and Richard Koche and Pierre-Jacques Hamard},
  journal = {STAR protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104916},
  url = {https://europepmc.org/article/PMC/PMC13718845},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Protocol for profiling chromatin accessibility in human small-cell lung cancer FFPE-derived samples using Omni-ATAC-seq
AU  - Eralda Salataj
AU  - Kenta Kawasaki
AU  - Joan Massagué
AU  - Charles M. Rudin
AU  - Iestyn Whitehouse
AU  - Richard Koche
AU  - Pierre-Jacques Hamard
PY  - 2026
DA  - 2026/10/23
JO  - STAR protocols
DO  - 10.1016/j.xpro.2026.104916
UR  - https://europepmc.org/article/PMC/PMC13718845
AB  - The assay for transposase-accessible chromatin using sequencing (ATAC-seq) on formalin-fixed paraffin-embedded (FFPE) samples maps accessible chromatin in archival tissues, but DNA degradation and crosslinking remain significant challenges when processing these samples. Here, we present a protocol for Omni-ATAC-seq on degraded human small-cell lung cancer (SCLC) FFPE-derived samples. We detail steps for successful nuclei isolation, efficient tagmentation, and optimal library amplification to overcome the low signal-to-noise ratio. This protocol enables high-quality epigenetic profiling, turning archived SCLC samples into valuable resources for studying disease progression.  For complete details on the use and execution of this protocol, please refer to Kawasaki et al.1
SN  - 2666-1667
ER  -