ArticleNature protocols2011
Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 62 citations in OpenAlex.
- EZH2 dependent H3K27me3 is involved in epigenetic silencing of ID4 in prostate cancer.Oncotarget · 2014Pooled it
- Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.Biological procedures online · 2025Article
- Building integrative functional maps of gene regulation.Human molecular genetics · 2022Article
- Article
- A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples.Bio-protocol · 2022Article
- The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues.International journal of molecular sciences · 2022Review
- FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.Nucleic acids research · 2021Article
- Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections.Molecular systems biology · 2021Article
- Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-International journal of molecular sciences · 2021Article
- Protoblock - A biological standard for formalin fixed samples.Microbiome · 2020Article
- Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq.BMC genomics · 2019Article
- TF-ChIP Method for Tissue-Specific Gene Targets.Frontiers in cellular neuroscience · 2019Article
- Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology.Clinical epigenetics · 2018Article
- Detection of Histone H3 mutations in cerebrospinal fluid-derived tumor DNA from children with diffuse midline glioma.Acta neuropathologica communications · 2017Article
- Tumour heterogeneity: principles and practical consequences.Virchows Archiv : an international journal of pathology · 2016Review
- High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue.Nature protocols · 2016Article
- Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells.Neuroepigenetics · 2016Article
- A novel nuclear Src and p300 signaling axis controls migratory and invasive behavior in pancreatic cancer.Oncotarget · 2016Article
- Common BRAF(V600E)-directed pathway mediates widespread epigenetic silencing in colorectal cancer and melanoma.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays.Analytical chemistry · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed, paraffin-embedded (FFPE) samples represent the gold standard for storage of pathology samples. Here we describe pathology tissue chromatin immunoprecipitation (PAT-ChIP), a technique for extraction and high-throughput analysis, by techniques such as ChIP-seq, of chromatin derived from FFPE samples. Technically, the main challenge of PAT-ChIP is the preparation of good-quality chromatin from FFPE samples. Here we provide a detailed explanation of the methodology used, the choice of reagents and the troubleshooting steps required to establish a robust chromatin preparation procedure. Other steps have also been adapted from existing techniques to optimize their use for PAT-ChIP-seq. The protocol requires 4 d from the start to the end of the PAT-ChIP procedure. PAT-ChIP provides, for the first time, the chance to perform analyses of histone modifications and transcription factor binding on a genome-wide scale using patient-derived FFPE samples. This technique therefore allows the immediate use of pathology archives (even those that are several years old) for epigenetic analyses and the identification of candidate epigenetic biomarkers or targets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.