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).

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 8 claims · 5 setups

  Has reproduction

  AOE integrates publicly available gene expression data from GEO, ArrayExpress, and GEA into a single searchable index.

  ebi ncbi sequence arrayexpress metadata cross-database visualization

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

  Full-text index only

  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

  PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups

  Full-text index only

  An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.

  biological 2de agml gel mass visualization

• Protein expression patterns in primary carcinoma of the vagina.

  PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

  Full-text index only

  Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

  fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read