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).

• Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.

  PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups

  Has reproduction · 91

  CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC

  pancreatic gse143754 pdac tcga microarray wgcna differential

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

  PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.

  hapmap genotype genotype raw case-control

• Mutation analysis of the Uromodulin gene in 96 individuals with urinary tract anomalies (CAKUT).

  PMID 18846391 · PMC3155267 · Pediatric nephrology (Berlin, Germany) · 2009 · 8 claims · 5 setups

  Full-text index only

  No UMOD mutations were identified in 96 patients with CAKUT after full mutation screening

  genomic pcr cakut direct cel sequencing

• SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.

  PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups

  Has reproduction · 82

  SMAGEXP integrates the metaMA and metaRNASeq R packages into Galaxy to provide a unified tool suite for transcriptomics meta-analysis.

  oral geo lung gene affymetrix limma

• Deep learning based protocol to construct an immune-related gene network of host-pathogen interactions in plants.

  PMID 36525344 · PMC9791427 · STAR protocols · 2023 · 6 claims · 6 setups

  Has reproduction · 96

  A deep-learning protocol (DLNet) ranks genes by their contribution to classifying treatment versus control expression data, identifying genes involved in host defense against pathogens.

  oryza rice merged top-ranked affymetrix microarray batch

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

  PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 7 claims · 3 setups

  Has reproduction · 30

  COMMAND>_ is a flexible multi-user web application that searches, downloads, parses, re-annotates, and imports gene expression experiments into a coherent data model.

  small user-defined microarray affymetrix rna-seq probe-to-gene

• Contrasting nutrient retention in alpine soils: the role of soil microbiome in phosphorus and nitrogen mobility in scree and meadow environments.

  PMID 41632073 · PMC12883989 · FEMS microbiology ecology · 2026 · 6 claims · 8 setups

  Has reproduction · 63

  Scree soils have high mobile nitrate and phosphate, low phosphate sorption ability, and significantly greater phosphorus leaching despite lower organic matter and microbial biomass

  scree dried fresh thawed situ organic colorimetry

• The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.

  PMID 36196618 · PMC9720673 · Development (Cambridge, England) · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Can-elt-3 (and orthologues in C. portoensis and C. monodelphis) is expressed in the early E lineage prior to elt-2 orthologue expression

  angaria elegans portoensis gata rnai single-molecule smifish