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).

• 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

• 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

• The reprogramming and function of H4K20me1 during early embryo development.

  PMID 42020515 · PMC13261155 · EMBO reports · 2026 · 7 claims · 8 setups

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  Low-input CUT&RUN (as few as 100 cells) reliably maps H4K20me1 and correlates strongly with conventional ChIP-seq

  k562 oocytes embryos zebrafish cut&run chip-seq immunofluorescence

• The SMARCA4 subunit of the SWI/SNF complex prevents genome instability at G quadruplexes.

  PMID 42002776 · PMC13224610 · Genome biology · 2026 · 7 claims · 7 setups

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  SMARCA4 binds genome-wide at G4-forming sequences, particularly at promoters and enhancers in open, actively transcribed chromatin

  rpe1 hek293t cut&run induce-seq genome

• 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

• 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

• 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

• RUVBL1 and RUVBL2 are druggable MYC effector regulators in neuroblastoma cells.

  PMID 41940329 · PMC13049659 · iScience · 2026 · 8 claims · 8 setups

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  RUVBL1 and RUVBL2 target gene sets are significantly depleted in MYCN-driven NB mouse tumors treated with ATR inhibitors (elimusertib, ceralasertib)

  th-mycn neuroblastoma clb-bar clb-ga rna-seq gene western

• Remodeling of XIST regulatory landscape during primate evolution.

  PMID 41544163 · PMC12810636 · Science advances · 2026 · 8 claims · 8 setups

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  XIST regulation has diverged uniquely and rapidly between closely related primates: JPX is a major XIST regulator in human and marmoset ESCs but only a minor regulator in macaque ESCs

  lyon-es1 rna-fish bulk capture

• 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

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• Stage-specific epigenetic priming amplifies gene activation during lineage commitment.

  PMID 41894493 · PMC13025117 · Science advances · 2026 · 8 claims · 8 setups

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  Full-body Msl1 knockout causes embryonic lethality by E10.5, with morphological/developmental delay detectable already at E8.5

  embryos e9.5 mesc-derived bright-field western 10x

• The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence.

  PMID 42118810 · PMC13189416 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  Differentiation of PUER progenitors into macrophages and neutrophils proceeds through cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic order.

  puer kit+ bulk scrna-seq cut&run