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 10

System / cell line: cut&run ✕ Assay: enrichment ✕ Clear

Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.

PMID 42206359 · PMC13216745 · Nucleic acids research · 2026 · 8 claims · 8 setups

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High GAF occupancy is required for chromatin looping and gene regulation at PREs

drosophila third gaf dac_tss cut&run micro-c hi-c
Mechanisms of gene regulation by SRCAP and H2A.Z.

PMID 41792122 · PMC13087030 · Nature communications · 2026 · 8 claims · 8 setups

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Acute SRCAP degradation causes rapid, genome-wide replacement of H2A.Z by canonical H2A, with turnover fastest at active promoters/enhancers and slower at bivalent loci

syat cut&run live h2a.z
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups

Has reproduction · 57

About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.

k562 hct116 subset chip-exo chip-seq western
Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.

PMID 40846763 · PMC12425804 · Nature genetics · 2025 · 8 claims · 8 setups

Has reproduction · 75

BRG1 binding to chromatin exhibits a linear, dose-dependent response to BRG1 protein levels, independent of TF or histone-modification co-occupancy

brg1-fkbp12-f36v brg1-knock-in mes snf2h-fkbp12-f36v western cut&run atac-seq
Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.

PMID 41650962 · PMC12985389 · Stem cell reports · 2026 · 8 claims · 8 setups

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Analysis of 532 RNA-seq datasets constructed a high-resolution promoter activity landscape across hematopoietic lineages

hematopoietic major monocytes candidate rna-seq h3k4me3 motif
Stage- and cluster-specific regulation of chondrogenic gene programs by Sox9 in mouse embryonic limb buds.

PMID 41809054 · PMC12969044 · iScience · 2026 · 8 claims · 7 setups

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scRNA-seq across five limb bud stages identifies four Sox9-high populations (chondroprogenitors 1, 2, 3, and mature chondrocytes) with distinct temporal dynamics

forelimb scrna-seq cut&run embryo single-cell cut&run velocity
Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.

PMID 41037662 · PMC12877751 · Cancer discovery · 2026 · 8 claims · 7 setups

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ATAC-seq profiling of osteosarcoma patient samples, PDXs, and PDX-CLs reveals two distinct chromatin accessibility subtypes: early osteoblast-derived (EOD) and late osteoblast-derived (LOD)

n=8 pdx-derived pdx osteosarcoma atac-seq bulk h3k27ac
Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

PMID 41738738 · PMC12935429 · eLife · 2026 · 8 claims · 8 setups

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LS-MPRA (BAC-based) and d-MPRA (systematic mutagenesis) are complementary methods for unbiased, high-resolution mapping of cis-regulatory modules.

mus e14 retina candidate ls-mpra single-cell individual
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

Has reproduction · 88

SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

kidney tubuloids immunodeficient tub rt-qpcr western histology
The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements.

PMID 41632506 · PMC12867480 · eLife · 2026 · 8 claims · 8 setups

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CHD4 acts via a second mechanism beyond nucleosome sliding: actively restricting the residence time of transcription factors on chromatin

chd4-maid sall1 western flow calibrated

Experiments

Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.

Mechanisms of gene regulation by SRCAP and H2A.Z.

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.

Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.

Stage- and cluster-specific regulation of chondrogenic gene programs by Sox9 in mouse embryonic limb buds.

Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.

Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements.