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

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• 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

• 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

• Nucleosome deposition and DNA methylation at coding region boundaries.

  PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.

  yeast drosophila resting naive nucleosome methylation pol

• 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

• 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

• 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

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

  Full-text index only

  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• 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

• 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

• Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

  PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

  nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa

• 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

• Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

  PMID 41620470 · PMC12963367 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  A three-step RAMPAGE-based pipeline can systematically identify TE-derived transcription start sites (TSSs) genome-wide, distinguishing them from autonomous TE transcription and background noise.

  biosamples same k562 genomic rampage rna-seq h3k4me3

• 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

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• 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

• Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer.

  PMID 41412800 · PMC12849445 · Genes & development · 2026 · 7 claims · 7 setups

  Full-text index only

  H3K9 methylation and the demethylase KDM4C, through association with SWI/SNF, drive proliferation of cells fated to become endocrine-resistant via a nongenomic estrogen-mediated mechanism

  parental t47d esr1 scrna-seq hi-c atac-seq