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).

• Chromatin accessibility directly governs flavonoid biosynthesis and indirectly orchestrates cannabinoid production in Cannabis.

  PMID 41635698 · PMC12861918 · Frontiers in plant science · 2025 · 8 claims · 5 setups

  Full-text index only

  Increased chromatin accessibility at promoters of flavonoid-biosynthetic genes up-regulates their expression, driving flavonoid accumulation in the H cultivar.

  inflorescences rna-seq untargeted bulk atac-seq

• Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

  PMID 41904529 · PMC13217986 · Cell communication and signaling : CCS · 2026 · 8 claims · 7 setups

  Full-text index only

  MITF knockdown and IFNγ stimulation each produce substantial but distinct changes in chromatin accessibility in 624Mel melanoma cells

  624mel melanoma atac-seq western motif

• 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

  Full-text index only

  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

• RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

  PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups

  Has reproduction · 63

  RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data

  embryonic cd34+ shared promoter rna-seq atac-seq gsea

• B-lineage commitment is dependent on a reversible epigenetic switch.

  PMID 41266087 · PMC12863259 · Genes & development · 2026 · 8 claims · 8 setups

  Full-text index only

  B-lymphoid commitment is mediated by a transcription factor-dose-dependent epigenetic switch that suppresses inherent T-lineage potential in early lymphoid progenitors

  bone expanded pax5 ebf1 combined atac-seq chip-seq

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

  Full-text index only

  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

  PMID 41746809 · PMC13042203 · Cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  UPF2-mediated NMD is required for proper cortical lamination; conditional Upf2 deletion in radial glia disrupts layering of TBR1+/SATB2+ and CTIP2+/CUX1+ neurons.

  cortex embryonic cortical neural immunofluorescence utero co-electroporation

• TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

  PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

  Full-text index only

  TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

  drosophila combined motif chip-seq whole-animal

• MECOM Function Is Critical for AR-Driven Treatment-Resistant Prostate Cancer.

  PMID 41529070 · PMC13136877 · Cancer research · 2026 · 7 claims · 8 setups

  Full-text index only

  EVI1, encoded by MECOM, is an AR-recruited coactivator of noncanonical AR signaling in prostate cancer.

  lrex lucap167 prostate live-cell spheroid patient-derived