ArticleNature communications2023
Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 33 citations in OpenAlex.
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- Spatially tunable multiomic sequencing using light-driven combinatorial barcoding of molecules in tissues.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT.Nature communications · 2026Article
- CDK12/CDK13 inhibition disrupts transcriptional elongation and replication fork progression in glioblastoma.EMBO molecular medicine · 2026Article
- Unraveling the complexity of the histone code: implications for gene regulation and disease.Genome biology · 2026Review
- Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF.Science advances · 2026Article
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- Epigenetic reprogramming in autoimmune and immune-mediated skin disease.Frontiers in immunology · 2026Review
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
- The rise of historical epigenomics and temporal analysis of gene regulation.Genome biology · 2025Review
- Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states.Nucleic acids research · 2025Article
- Review
- Total whole-arm chromosome losses predict malignancy in human cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Global modulation of gene expression and transcriptome size in aneuploid combinations of maize.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Proposal of a Safe Transport Protocol and Its Utility of Antigen-Preserving Tissue for Formalin-Fixed Porcine Renal Samples.Biomedicines · 2025Article
- Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing.Nucleic acids research · 2025Article
- RNA polymerase II at histone genes predicts outcome in human cancer.Science (New York, N.Y.) · 2025Article
- Application of Spatial Omics in the Cardiovascular System.Research (Washington, D.C.) · 2025Review
- Benchmark of chromatin-protein interaction methods in haploid round spermatids.Frontiers in cell and developmental biology · 2025Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
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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.