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).

• A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

  PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).

  hand-sorted drosophila chip-seq immunostaining dapi

• 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

• Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.

  PMID 40758707 · PMC12333995 · PLoS pathogens · 2025 · 8 claims · 7 setups

  Has reproduction · 90

  Six viral promoters (UL5, UL72, EP3, UL57-AS, US16-AS, US30-S) are ≥50-fold more active in D-NT2 than in HFF at 96 h post-infection and are classified as viral long promoters.

  d-nt2 hcmv-infected hcmv pro-seq dff-chip promoter

• 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

• High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

  PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups

  Has reproduction · 87

  mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.

  c57bl strand-specific pol computational

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• 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

• 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

• Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

  PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

  pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see

• iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.

  PMID 41499218 · PMC12777978 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

  Has reproduction · 53

  iceDP is a tool that uses the Density Peaks clustering algorithm plus a distribution test and fold-change filter to identify non-homologous inter-chromatin contacts (NHCCs) from Hi-C data

  olfactory mosn hesc type in-situ h3k27ac micro-c