ArticleEpigenetics & chromatin2018
Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs.
Article in Epigenetics & chromatin, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.STAR protocols · 2026Article
- Androgen receptor imprints satellite cell stemness and preserves their reservoir for lifelong regeneration and optimal repair.Science advances · 2026Article
- Evidence for coordinate CTCF and histone H3.3 activities in K27M diffuse midline gliomas.Acta neuropathologica communications · 2026Article
- Intra species dissection of phytophthora capsici resistance in black pepper.Journal of advanced research · 2025Article
- Chromatin-bound U2AF2 splicing factor ensures exon inclusion.Molecular cell · 2025Article
- MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues.Science advances · 2025Article
- Plasma Cell-Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer.Cancer research · 2025Article
- MLL oncoprotein levels influence leukemia lineage identities.Nature communications · 2024Article
- Article
- A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies.Genes & development · 2024Article
- Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells.EBioMedicine · 2024Article
- UNADON: transformer-based model to predict genome-wide chromosome spatial position.Bioinformatics (Oxford, England) · 2023Article
- In situ tools for chromatin structural epigenomics.Protein science : a publication of the Protein Society · 2022Article
- EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.Bioinformatics (Oxford, England) · 2022Article
- CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells.Genome biology · 2022Article
- Article
- CUT&RUN Profiling of the Budding Yeast Epigenome.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Simultaneous profiling of multiple chromatin proteins in the same cells.Molecular cell · 2021Article
- Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia.Nature genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundOur understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution.
resultsHere, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs.
conclusionsThe easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.
Indexed as
Identifiers
What OpenQuestion holds
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.