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).

• Genomic and proteomic techniques applied to reproductive biology.

  PMID 11574051 · PMC138959 · Genome biology · 2001 · 8 claims · 8 setups

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  Knockout of the E6-AP (UBE3A) gene reduces testis and prostate size in male mice and compromises estradiol action in females

  e6-ap fgf9-deficient jsd one-cell gene germ-cell interference

• Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

  PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

  Has reproduction · 80

  928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

  burkholderia pseudomallei bulk tmt-based rt-qpcr

• GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.

  PMID 41769841 · PMC12970594 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Incomplete/inaccurate gene annotations, especially missing or truncated 3' UTRs, cause reads to map to non-genic regions and genes to be under-quantified or missing from scRNA-seq expression matrices in non-model species

  genomes whole-organism xenia octopus peak scrna-seq

• The seeker R package: simplified fetching and processing of transcriptome data.

  PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging

  liver microarray rna-seq

• PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells.

  PMID 41694110 · PMC12902810 · Experimental and therapeutic medicine · 2026 · 7 claims · 7 setups

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  PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells

  h9c2 rt-qpcr western counting

• Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

  PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

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  Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

  cd4+ hela influenza-infected liver cdna microarray mass

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

  PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

  one nci60 cerevisiae cancer multidimensional cellular two-color

• 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