ArticleNature communications2018
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Post-translational modifications in the oral microenvironment: Stem cell regulation from periodontal regeneration to oral cancer therapy.World journal of stem cells · 2025Review
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
- Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis.Genome biology · 2025Article
- Article
- Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation.Proceedings. Biological sciences · 2024Review
- Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges.ACS omega · 2024Review
- scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting.Briefings in bioinformatics · 2023Article
- Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells.Cell death & disease · 2023Article
- Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity.Clinical epigenetics · 2023Review
- The technological landscape and applications of single-cell multi-omics.Nature reviews. Molecular cell biology · 2023Review
- Decoding Human Biology and Disease Using Single-cell Omics Technologies.Genomics, proteomics & bioinformatics · 2023Review
- Systematic pan-cancer analysis identifies SLC35C1 as an immunological and prognostic biomarker.Scientific reports · 2023Article
- Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.Science advances · 2023Article
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies.Developmental cell · 2023Article
- System analysis based on the lysosome-related genes identifies HPS4 as a novel therapy target for liver hepatocellular carcinoma.Frontiers in oncology · 2023Article
- Characterizing cis-regulatory elements using single-cell epigenomics.Nature reviews. Genetics · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor 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.