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).

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

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  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• 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

• Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

  PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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  A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

  drosophila genome melanogaster real-time comparative gfp

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.

  PMID 19864251 · PMC2811011 · Nucleic acids research · 2010 · 7 claims · 8 setups

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  SPEX-type approaches preferentially access genetic information from damaged, degraded endogenous ancient DNA templates over modern human contaminant DNA

  iceman hb50 pe168 lq4 relative pcr spex

• Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

  PMID 41664139 · PMC12888363 · Molecular horticulture · 2026 · 7 claims · 7 setups

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  Red-fleshed and orange-fleshed Guanxi pomelo arose from two independent somatic mutation events from the same white-fleshed wild type

  pomelo wild-type rt-qpcr carotenoid genome

• Loss of Ezh2 promotes M2-like macrophage polarization in hepatocellular carcinoma.

  PMID 41869562 · PMC12999353 · iScience · 2026 · 8 claims · 7 setups

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  Hepa1-6 conditioned media (CM) induces M2-like polarization of BMDMs in a dose-dependent manner

  bmdms rt-qpcr western flow

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a novel promoter motif enriched in TATA-less CpG island-associated promoters of ribosomal protein and housekeeping genes

  k562 hek293t hek293t-derived motif gro-cap luciferase

• Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

  PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

  hepg2 liver chip-seq quantitative co-immunoprecipitation

• Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

  PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups

  Has reproduction · 81

  Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR

  escs esc sequence compiled allele-specific chip-seq motif

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.

  PMID 40811813 · PMC12830129 · Blood advances · 2026 · 6 claims · 8 setups

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  Bex1 (and to a lesser extent Bex4) is ectopically expressed in Pten-deficient mouse T-ALL blasts

  thymocytes thymocyte t-all normal scrna-seq rt-qpcr bulk

• Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming.

  PMID 41606307 · PMC12945694 · Nature metabolism · 2026 · 8 claims · 8 setups

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  Lamin A/C represses cysteine biosynthesis and catabolism in naive mES cells by suppressing CTH and CBS

  mes metabolomics atac-seq chip-qpcr

• MerTK-triggered TGFβ1 autocrine signal regulates microglial response to neurodegeneration.

  PMID 41634038 · PMC12976283 · Nature communications · 2026 · 8 claims · 8 setups

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  Microglial response to pathological axonal degeneration (optic nerve injury) depends on the phagocytic receptor MerTK

  optic facs-sorted microglia co-immunostaining qpcr bulk

• 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

• TBP regulates transposable element expression in early mouse embryos.

  PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

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  The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

  single embryos computational embryonic rna-seq atac-seq motif

• RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

  PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

  hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq

• Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

  PMID 41515103 · PMC12787715 · Plants (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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  295 AP2/ERF transcription factor genes were identified and classified in the S. scabra genome

  scabra representative hmm rna-seq qpcr

• Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• 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