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).

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

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

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  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

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.

  PMID 35580127 · PMC9159589 · PLoS genetics · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Pigmentation genes are only expressed in mitfa-expressing zebrafish melanocyte-lineage cells that also express tfap2 paralogs

  gfp+ sk-mel-28 tfap2a single-cell crispr atac-seq

• A computational pipeline to visualize DNA-protein binding states using dSMF data.

  PMID 35463472 · PMC9026571 · STAR protocols · 2022 · 8 claims · 2 setups

  Has reproduction · 89

  The pipeline maps states of protein-binding DNA in vivo using dSMF data and identifies binding states at an enhancer in Drosophila S2 cells

  drosophila dual-enzyme starr-seq

• miRGen 2.0: a database of microRNA genomic information and regulation.

  PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

  lung organ malme embryonic polii small nucleosome