ArticleNucleic acids research2024
Low-input and single-cell methods for Infinium DNA methylation BeadChips.
Article in Nucleic acids research, 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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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.
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Who cites it
19 citing papers in PubMed, 22 citations in OpenAlex.
- Sellar region neurocytomas exhibit a CIMP and neuroendocrine-like epigenetic signature distinct from other intra-axial neurocytomas.Acta neuropathologica · 2026Article
- TET1 noncatalytic activity shapes the chromatin landscape associated with de novo methylation establishment in the male germline.Genes & development · 2026Article
- Placental Methylation Profile in Women Exposed to Fluoride and Its Association with Kidney Volume at Birth.Clinical journal of the American Society of Nephrology : CJASN · 2026Article
- Ultra-low oxygen tension duringbioRxiv : the preprint server for biology · 2026Article
- DNA Methylation-Based Risk Stratification and Classification of Pediatric Thyroid Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- DNA methylation changes in thyroid cancer patients infected with SARS-CoV-2.Updates in surgery · 2026Article
- Global Hypomethylation in Cell-Free DNA Enables Noninvasive Colorectal Cancer Screening: Results from a Retrospective Validation Study.Computational and structural biotechnology journal · 2026Article
- Epi-liquidomics: redefining cancer diagnostics through epigenetic profiling.Frontiers in epigenetics and epigenomics · 2026Review
- DNA methylation signatures of frailty beyond age: a longitudinal study of female and male mice.bioRxiv : the preprint server for biology · 2025Article
- KnowYourCG: Facilitating base-level sparse methylome interpretation.Science advances · 2025Article
- A ternary-code DNA methylome atlas of mouse tissues.Genome biology · 2025Article
- Scalable screening of ternary-code DNA methylation dynamics associated with human traits.Cell genomics · 2025Article
- Artificial intelligence for comprehensive DNA methylation analysis: overview, challenges, and future directions.Briefings in bioinformatics · 2025Review
- Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.Biological procedures online · 2025Article
- Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis.Epigenomes · 2025Article
- mLiftOver: harmonizing data across Infinium DNA methylation platforms.Bioinformatics (Oxford, England) · 2024Article
- A critical review of the recent concept of regulatory performance of DNA Methylations, and DNA methyltransferase enzymes alongside the induction of immune microenvironment elements in recurrent pregnancy loss.Toxicology reports · 2024Review
- A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.Nature communications · 2024Article
- Treatment with novel topoisomerase inhibitors in Ewing sarcoma models reveals heterogeneity of tumor response.Frontiers in cell and developmental biology · 2024Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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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.