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).

Publications 1.3k Datasets 392.5k Experiments 6

System / cell line: cluster ✕ Assay: histology ✕ Clear

Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

Has reproduction · 100

S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

gastric colorectal additional breast xenium visium histology
A taxonomy of epithelial human cancer and their metastases.

PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

epithelial tumor metastatic breast microarray gene fisher
Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

lung gene differentially significantly laser histology principal
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

Has reproduction · 69

Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

colon gut single-cell 16s western
Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 90

Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

sural peripheral snrna-seq nerve single-nucleus subcellular situ
Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

Has reproduction · 93

snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

interscapular ibat bat single-nucleus qpcr western

Experiments

Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

A taxonomy of epithelial human cancer and their metastases.

Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.