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).

• Toward stem cell systems biology: from molecules to networks and landscapes.

  PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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  Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

  stem embryonic promyelocytic genome-wide serial chip-chip

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

  PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups

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  Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.

  escs fibroblasts hematopoietic bxd transcriptional forced long-term

• Rats go genomic.

  PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

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  A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

  recombinant genes serotonin adenomatous genome-wide targeted knockout

• Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

  PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  The S. Adjame outbreak produced a heterogeneous phylogeny with multiple temporally/geographically linked sub-clusters, atypical of a point-source Salmonella outbreak and consistent with contamination from an endemic mixed-strain source (imported South Asian herbs/spices).

  salmonella adjame outbreak commonly genome reference-based cgmlst

• Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

  PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 7 setups

  Has reproduction · 73

  Probe-specific upper and lower thresholds for flagging aberrant DNA methylation can be derived from a reference database of >2,000 normal and tumour-adjacent normal samples spanning 25 tissue types.

  blood tcga gse40279 most illumina supervised unsupervised