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).

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

  PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

  hff mrc5 chip-qpcr rt-qpcr chipseq

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.

  PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups

  Has reproduction · 67

  NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.

  e14 mass western net-prism

• Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.

  PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release

  cortical transcribed reconstituted erna-bound gro-seq exo-seq shape-map

• β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia.

  PMID 36597789 · PMC9906382 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  β-catenin binds directly to promoters of RNA processing, splicing, and ribosomal biogenesis genes in T-ALL cells

  rpmi8402 chipseq chip-qpcr sequencing

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq