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).

• Enteroendocrine cell lineages that differentially control feeding and gut motility.

  PMID 36810133 · PMC10032656 · eLife · 2023 · 6 claims · 8 setups

  Has reproduction · 88

  Vil1-p2a-FlpO knock-in mice combined with lineage-specific Cre lines enable highly selective intersectional genetic access to major enteroendocrine cell lineages (serotonin/enterochromaffin, GLP1, CCK, somatostatin, GIP) in vivo

  neurod1-cre neurog3-cre intestinal vil1-p2a-flpo single-cell fluorescence-activated two-color

• Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

  PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

  dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount

• Genetics and environment distinctively shape the human immune cell epigenome.

  PMID 41593234 · PMC12900638 · Nature genetics · 2026 · 8 claims · 6 setups

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  Exposure-associated differentially methylated regions (eDMRs) and genotype-associated DMRs (gDMRs) show distinct genomic distributions: eDMRs are enriched at enhancers/regulatory regions, while gDMRs are predominantly found in gene bodies.

  pbmcs pbmc edmrs differentially single-nucleus fluorescence-activated motif

• Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.

  PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups

  Has reproduction · 95

  Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism

  drosophila reactome kegg gene fluorescence manual

• The use of neuroproteomics in drug abuse research.

  PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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  Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

  rodent brain postmortem sectioned 2d-dige itraq heat

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

  PMID 36450262 · PMC9792173 · Cell reports · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

  cd44+ splenocytes spleen tcr scrna-seq flow spatial

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Single-cell transcriptomics reveals keratinocyte dynamic processes associated with S100a4 expression in psoriasiform dermatitis.

  PMID 41660613 · PMC12876221 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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  S100a4 knockout mice show significant pathological improvement in psoriasis-like lesions, including reduced inflammatory cell infiltration and decreased epidermal hyperplasia

  c57bl skin dorsal dcmo crispr western imiquimod-induced

• Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis.

  PMID 41741465 · PMC13057173 · Nature communications · 2026 · 8 claims · 7 setups

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  The MTOR eQTL variant rs4845987 has context-specific, opposite effects on MTOR expression: decreasing it in activated T cells and increasing it in neutrophils.

  blood bulk eqtl sepsis bulk cell-type colocalisation

• Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution.

  PMID 41513700 · PMC12891662 · Nature communications · 2026 · 8 claims · 8 setups

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  Cytomix (TNFɑ+IFNɣ+IL1β) treatment of human colon organoids best recapitulates molecular features of human IBD compared to DSS or irradiation injury models.

  colon cytomix-treated scrna-seq immunofluorescence activated

• 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

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• AJUBA: The Master Regulator Bridging EMT and Immune Evasion in Colorectal Cancer.

  PMID 41814682 · PMC13140425 · Mediators of inflammation · 2026 · 8 claims · 8 setups

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  AJUBA is markedly upregulated in CRC across multiple transcriptomic cohorts and is enriched in epithelial cells with activated EMT features

  tcga-crc crc paired hct116 bulk single-cell spatial