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).

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• 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

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

  v6.5 mes icshape rt-qpcr western

• Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

  PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

  Full-text index only

  Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

  cos-7 293t synthetic pms2 shuttle primer steady-state

• Mosaicism in von Hippel-Lindau disease: an event important to recognize.

  PMID 18205710 · PMC4401302 · Journal of cellular and molecular medicine · 2007 · 7 claims · 5 setups

  Full-text index only

  The proband's father is a somatic mosaic for a VHL missense mutation (R161Q), explaining his mild, late-onset phenotype compared to his daughter's severe early-onset disease.

  peripheral father's pcr proband dhplc sanger semiquantitative

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

  Full-text index only

  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic