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).

• 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

• BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.

  PMID 15653630 · PMC546182 · Nucleic acids research · 2005 · 7 claims · 4 setups

  Full-text index only

  BiSearch is a new web-available primer-design software for bisulfite-treated genomes that also analyzes primer pairs for mispriming sites via a novel search algorithm.

  tyrosine homo hek primer post-design pcr

• A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

  PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

  chimpanzee hepg2 promoters liver quantitative western sirna

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

  Full-text index only

  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 79

  CLSM6A is a set of CNN-based deep learning models that predict single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  hct116 a549 brain hek293t miclip m6a-clip-seq m6a-seq

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq