Peer-reviewedCC BY-NCSTAR protocols
Protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections and constructing sequencing libraries.
4 affiliations
- 1Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. Electronic address: [email protected].
- 2Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
- 3Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
- 4Institute of Innovative Drug, China Pharmaceutical University, Nanjing 211134, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China. Electronic address: [email protected].
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are archived resources for biomedical research but challenging for single-cell transcriptomic analysis. Here, we present a protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections. We describe steps for deparaffinization, enzymatic digestion, nuclei purification, and library construction using the 10× Genomics Fixed RNA Profiling platform. This protocol enables transcriptomic profiling of archived clinical specimens at single-nucleus resolution. For complete details on the use and execution of this protocol, please refer to Chen et al.¹.
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BibTeX
@article{ning2026protocol,
title = {{Protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections and constructing sequencing libraries.}},
author = {Huiheng Ning and Wei Zhou and Kang Chen and Qinhang Gao and Jieying Pan and Min-Min Chen},
journal = {STAR protocols},
year = {2026},
month = oct,
doi = {10.1016/j.xpro.2026.104880},
url = {https://europepmc.org/article/MED/42848517},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections and constructing sequencing libraries.
AU - Huiheng Ning
AU - Wei Zhou
AU - Kang Chen
AU - Qinhang Gao
AU - Jieying Pan
AU - Min-Min Chen
PY - 2026
DA - 2026/10/08
JO - STAR protocols
DO - 10.1016/j.xpro.2026.104880
UR - https://europepmc.org/article/MED/42848517
AB - Formalin-fixed paraffin-embedded (FFPE) tissues are archived resources for biomedical research but challenging for single-cell transcriptomic analysis. Here, we present a protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections. We describe steps for deparaffinization, enzymatic digestion, nuclei purification, and library construction using the 10× Genomics Fixed RNA Profiling platform. This protocol enables transcriptomic profiling of archived clinical specimens at single-nucleus resolution. For complete details on the use and execution of this protocol, please refer to Chen et al.¹.
SN - 2666-1667
ER -