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).

• 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

• 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

• 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

• 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

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  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

• Sequencing the regulatory genome.

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

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  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

• Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

  PMID 41735587 · PMC12987734 · Nature genetics · 2026 · 8 claims · 8 setups

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  Pico-C, a low-input Micro-C method, enables high-resolution, temporally resolved 3D genome mapping in early Drosophila embryos using as few as ~60,000 nuclei

  hand-staged early drosophila pico-c chip-seq atac-seq