Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 16

System / cell line: per ✕ Assay: snatac-seq ✕ Clear

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

PMID 42030938 · PMC13198283 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A multiomic (snRNA-seq, snATAC-seq, WGS, CODEX) atlas defines a core set of pHGG neoplastic cell states shared across molecular subtypes

phgg neoplastic fetal single-nucleus whole-genome codex
Semi-parametric empirical bayes method for multiplet detection in snATAC-seq with probabilistic multi-omic integration.

PMID 42054434 · PMC13148828 · PLoS computational biology · 2026 · 8 claims · 5 setups

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SEBULA models the singlet background directly from observed HCLC (high-coverage locus count) statistics using fragment-level snATAC-seq information, avoiding reliance on synthetic/artificial doublets.

dogma-seq dogma-seq-derived seven snatac-seq q-q density
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

gastrulating gastrula gold-standard embryo single-cell computational promoter
Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

PMID 41632074 · PMC12954174 · GigaScience · 2026 · 8 claims · 5 setups

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Generated a multi-organ snATAC-seq atlas of 9 adult rat organs comprising 25 libraries and over 110,000 cells

organs publicly snatac-seq group-level snatac-seq scrna-seq gene
Shared genetic and neuroimmune architecture links type 1 diabetes with neurocognitive traits.

PMID 41826324 · PMC13139607 · Nature communications · 2026 · 8 claims · 8 setups

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T1D GWAS heritability is enriched in accessible chromatin of brain-resident cells, most notably microglia, across neurodevelopment into adulthood

cortex single-nucleus gwas gtex stratified scavenge s-ldsc
Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma.

PMID 41865105 · PMC13144680 · Scientific reports · 2026 · 8 claims · 5 setups

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snATAC-seq resolves cell-type specific chromatin accessibility, microRNA activity, transcription factor networks, and super enhancer usage in FLC tumors versus non-malignant liver (NML).

flc bulk snatac-seq snrna-seq single-nucleus bulk motif
Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

postmortem million+ pfc each single-nucleus umap pseudobulk
Single-cell resolution of an open chromatin signature in persister tumor cells.

PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

non-malignant same epithelial tumor single-nucleus mitochondrial copy-number
Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

pbmcs pbmc classical cmono single-nucleus differential multimodal
Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

PMID 41857393 · PMC13061643 · Nature neuroscience · 2026 · 8 claims · 6 setups

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Adult spinal-cord-derived human oligodendroglia and astrocytes, but not microglia, show primed chromatin signatures at HOX loci and a putative SOX10 enhancer.

postmortem induced lentiviral cns single-nucleus nanocut&tag high-resolution
Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
Single-cell spatiotemporal dissection of the human maternal-fetal interface.

PMID 41951740 · PMC13149032 · Nature · 2026 · 8 claims · 8 setups

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Generated a comprehensive single-cell multiomic and spatial atlas of the human maternal-fetal interface from early gestation to term

decidua maternal-fetal pseudobulk trophoblast paired genotype snatac-seq
Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

PMID 41758930 · PMC13197979 · Blood · 2026 · 8 claims · 6 setups

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Orca-T immunotherapy leads to increased phenotypic T-cell activation compared with unmanipulated PBSC grafts, persisting for months after treatment.

peripheral sorted fresh cryopreserved flow single-cell tcr
Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

PMID 41782826 · PMC12955150 · iScience · 2026 · 8 claims · 6 setups

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Tet2-deficient NOD mice transplanted with WT bone marrow show fewer islet-infiltrating lymphocytes beginning 8–10 weeks post-transplant, primarily among CD4+ T cells

islets islet islet-infiltrating cadaveric flow single-cell single-nucleus
An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

PMID 41937210 · PMC13067603 · Genome biology · 2026 · 8 claims · 8 setups

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Constructed an integrated multiomic atlas of the human left ventricle combining ~2.3M snRNA-seq nuclei from 299 donors and ~690K snATAC-seq nuclei from 106 donors

left heart cardiac snrna-seq snatac-seq bulk

Experiments

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

Semi-parametric empirical bayes method for multiplet detection in snATAC-seq with probabilistic multi-omic integration.

Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

Shared genetic and neuroimmune architecture links type 1 diabetes with neurocognitive traits.

Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma.

Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

Single-cell resolution of an open chromatin signature in persister tumor cells.

Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

Single-cell spatiotemporal dissection of the human maternal-fetal interface.

Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.