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).

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• SexTumorDB: a comprehensive resource of sex-dependent tumor landscape at single-cell resolution.

  PMID 41741497 · PMC13046873 · Scientific data · 2026 · 7 claims · 8 setups

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  SexTumorDB is an integrated resource of RNA-seq profiles of non-reproductive tumors at single-cell resolution, curated, processed, and standardized from published datasets

  acute bladder clear colorectal scrna-seq snrna-seq

• Dissecting gene regulatory networks governing human cortical cell fate.

  PMID 41565813 · PMC12999477 · Nature · 2026 · 8 claims · 6 setups

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  ZNF219, a previously uncharacterized transcription factor, represses neural differentiation in human cortical radial glia

  cortical rhesus single-cell scrna-seq immunocytochemistry

• Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

  PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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  Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

  tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell

• 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

• Molecular signatures of cell diversity modulated by long noncoding RNAs in the human fetal spinal cord.

  PMID 42006319 · PMC13090696 · iScience · 2026 · 8 claims · 7 setups

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  Three neural stem cell (NSC) lineages (NSC1, NSC2, NSCs) were annotated in the human fetal spinal cord

  fetal nsc2 scrna-seq scstereo velocity

• Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

  PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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  cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

  discoideum single-cell scrna-seq dissecting

• Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson's and inflammatory bowel disease.

  PMID 41545356 · PMC12847817 · NPJ Parkinson's disease · 2026 · 8 claims · 5 setups

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  Spatial single-cell multiomic imaging of sigmoid colon reveals both shared and unique features of peripheral immune dysfunction in PD and IBD

  sigmoid plasma stool epithelial cosmx meso gene

• Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.

  PMID 41675929 · PMC12886473 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 2 setups

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  Both innate and adaptive immune responses were activated in M. fortis peripheral blood at 10 dpi, while activation was not obvious in Kunming mice at the same time point

  pbmcs single-cell qpcr

• Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.

  PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 7 claims · 6 setups

  Has reproduction · 93

  ADICT (age-related decrease in transcriptome conservation) is commonly found in ageing tissues of nonmammalian species, including chicken brain, killifish liver and skin, and fruit fly brain

  drosophila nothobranchius gallus heterocephalus bulk single-cell

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

  PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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  MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

  lung ffpe lymph nonhuman scrna-seq spatial bulk

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• A cell atlas of multiple liver organoids and the fetal liver based on scRNA-seq.

  PMID 41736863 · PMC12927097 · iScience · 2026 · 8 claims · 8 setups

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  A unified liver organoid cell atlas of 217,025 high-quality cells was constructed by integrating scRNA-seq data from 15 organoid samples across 9 studies with human fetal liver data (5-19 weeks gestation)

  liver fetal endoderm-derived mesoderm-derived scrna-seq pseudotime pearson

• Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

  PMID 42010880 · PMC13096584 · Aging cell · 2026 · 8 claims · 8 setups

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  T cells are the immune cell population with the most pronounced transcriptomic alterations during liver aging

  liver nash cirrhotic hcc scrna-seq snrna-seq stereo-seq

• Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.

  PMID 42013848 · PMC13198233 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Consensus meta-program (MP) expression patterns stratify LUAD patients with rare and reference oncogenic mutations into ICI-MP-H and ICI-MP-L subgroups reflecting differential predicted ICI benefit

  luad matched tcga epithelial single-cell multiplex bulk

• MECP2 mutations rewire human ESC fate and bias cortical lineage commitment.

  PMID 42030940 · PMC13163216 · Stem cell reports · 2026 · 8 claims · 8 setups

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  MECP2 mutations induce an early naïve-like transcriptional drift in human ESCs, marked by upregulation of ZFP42/REX1 and other naïve-enriched markers

  isogenic undifferentiated 3-month bulk bulk single-cell single-nucleus

• Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

  PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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  LUSC arising within UIP originates from AT2-derived metaplastic basal cells

  fresh-frozen same scrna-seq paired single-cell copy ligand-receptor

• Dynamics of severity-associated immune remodeling by granulocytes and macrophages in acute lung injury.

  PMID 42111184 · PMC13157102 · iScience · 2026 · 7 claims · 7 setups

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  Granulocytes expand while macrophages are depleted as ALI severity progresses from intermediate to late stage

  bronchoalveolar granulocytes granulocyte immune single-cell gene pseudotime