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).

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

• Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

  PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

  genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin

• Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

  PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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  Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

  mm.1s pcr demethylating quantitative

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Protein microarray technology.

  PMID 17126887 · PMC1828913 · Mechanisms of ageing and development · 2007 · 8 claims · 8 setups

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  Protein microarrays enable high-throughput characterization of protein biochemical activities across an entire proteome in a single experiment

  yeast sh2 protein-protein protein-dna chromatin

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• 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

• Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

  PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

  hepg2 recombinant co-immunoprecipitation immunofluorescence gst