ReviewNature protocols2024
Scalable single-cell profiling of chromatin modifications with sciCUT&Tag.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- The response to kidney injury is epigenetically regulated through the activation of bivalent genes.American journal of physiology. Renal physiology · 2026Article
- Sequential RNA polymerase II activation drives human hematopoiesis.Cell reports · 2026Article
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- Review
- CUT&TIME captures the history of open chromatin in developing neurons.bioRxiv : the preprint server for biology · 2025Article
- Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq.Nature protocols · 2025Review
- Review
- NanoTag is an improved method to map interactions between DNA and proteins not requiring IgG.Scientific reports · 2025Article
- IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.Genome biology · 2025Article
- Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.Nucleic acids research · 2025Article
- Enhancer Enh483 regulates myoblast proliferation and differentiation of buffalo myoblasts by targeting FAXC.Cell and tissue research · 2025Article
- Review
- Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes.bioRxiv : the preprint server for biology · 2024Article
- The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping.Briefings in bioinformatics · 2024Article
- Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells.Journal of biological methods · 2024Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.
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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.