ArticleCommunications biology2020
ATAC-seq with unique molecular identifiers improves quantification and footprinting.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Systematic benchmarking of CUT&Tag improves the reliability and reproducibility of chromatin analysis.Cell reports methods · 2026Article
- Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.Nature communications · 2026Article
- Profiling chromatin accessibility responses to seasonal heat stress in Angora rabbit testes.BMC genomics · 2026Article
- PlantCTCIP: Chromatin Interaction Prediction Using Convolutional Neural Network and Transformer in Plants.Plant biotechnology journal · 2026Article
- SLUR(M)-py: a SLURM powered Pythonic pipeline for parallel processing of 3D (Epi)genomic profiles.Epigenomics · 2025Article
- Commentary on 'Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments'.Nucleic acids research · 2025Article
- Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity.Nature communications · 2025Article
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 2025Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- Characterization of the DNA accessibility of chloroplast genomes in grasses.Communications biology · 2024Article
- Single-cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines inMicrobiology spectrum · 2024Article
- A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.BMC biology · 2024Article
- Capture of regulatory factors via CRISPR-dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis.Nature plants · 2024Article
- Article
- Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice.Nucleic acids research · 2023Article
- Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.Genome biology · 2022Article
- Mapping open chromatin by ATAC-seq in bread wheat.Frontiers in plant science · 2022Article
- PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants.Nucleic acids research · 2021Article
- Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing.Biology · 2021Review
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq in our study. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq .
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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.