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).

• The archives are half-empty: an assessment of the availability of microbial community sequencing data.

  PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 6 setups

  Has reproduction · 95

  A large proportion of 16S rRNA amplicon sequencing studies contain data that is not available or not reusable despite being reported as deposited.

  publications randomly studies v3–v4 literature manual database

• Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

  PMID 32463383 · PMC7734503 · Journal of integrative bioinformatics · 2020 · 7 claims · 4 setups

  Has reproduction · 78

  Public fungal metabarcoding raw DNA data and their associated environmental metadata in sequence archives are heterogeneously annotated and lack a uniform processing pipeline, preventing large-scale biodiversity/distribution assessments.

  selected pubmed sra collection-site pdf pubmed sra

• MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

  PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

  chip-chip sequence genbank

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

  Full-text index only

  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• Proteomic-based identification of maternal proteins in mature mouse oocytes.

  PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

  mature mii identified tissues sds-page acid gene