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).

• 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

• Tumor reactivity assessment using clonal expression reveals tumor reactive CD8(+) T cell heterogeneity across solid tumors.

  PMID 42079667 · PMC13128579 · Frontiers in immunology · 2026 · 8 claims · 5 setups

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  TRACE, a clonotype-level CD8+ TRT classifier trained on an aggregated multi-study dataset, achieves robust holdout performance (mean MCC 0.84, F1 0.85)

  cd8+ expanded aggregated combined scrna-seq co-culture gene

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

  memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc

• Mapping the Development of Human Spermatogenesis Using Transcriptomics-Based Data: A Scoping Review.

  PMID 39000031 · PMC11241379 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

  Has reproduction

  scRNA-seq of human testis reveals major transcriptional modifications occurring around 11 years of age, marking a transition toward the adult cellular state

  fetal neonatal prepubertal peripubertal scrna-seq

• Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit.

  PMID 41501466 · PMC12820784 · Nature · 2026 · 8 claims · 8 setups

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  Inflammation-associated fibroblasts (IAFs), induced by proinflammatory FCN1+IL1B+ macrophages, produce profibrotic IL-11 and drive fibrosis in IBD

  intestinal colon pdgfra+ colonic scrna-seq xenium masson's

• The transcription factor HHEX maintains glucocorticoid levels and protects adrenals from androgen-induced lipid depletion.

  PMID 41519914 · PMC12891536 · Nature communications · 2026 · 8 claims · 8 setups

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  HHEX is the most enriched transcription factor in glucocorticoid-producing zona fasciculata (zF) cells, conserved across mouse, rat, and human adrenal

  sf1-cre-high adrenocortical scrna-seq rnascope immunohistochemistry

• Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

  PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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  SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

  hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

  PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

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  CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

  colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex

• The GENEVA platform models tumor mosaicism to reveal variations of responses to KRAS inhibitors and identify improved drug combinations.

  PMID 41735640 · PMC13035475 · Nature cancer · 2026 · 8 claims · 8 setups

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  GENEVA is a scalable single-cell-resolution platform for measuring drug responses across genetically diverse pooled 2D/3D cultures and xenograft models

  pooled pool nsg mosaic scrna-seq crispri mitotracker

• CAR-M2 immunotherapy resolves renal fibrosis via revascularization and apoptosis of profibrotic Cxcr2(+) endothelial cells.

  PMID 41887221 · PMC13130657 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CAR-M2 macrophages (anti-FAP CAR + IL-4-secreting, 4-1BB/CD3ζ costimulatory domains) specifically target and phagocytose FAP+ fibroblasts

  kidney car-m2 macrophages uuo scrna-seq histology live-cell

• Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization.

  PMID 41940331 · PMC13049529 · iScience · 2026 · 8 claims · 7 setups

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  Cellular composition at seeding (PD vs. BAL vs. Mixed) directs epithelial fate and immune polarization in organoid culture

  lung day organoid epithelial scrna-seq brightfield h&e

• Identification of cycling regulatory T cell precursors as conductors of immune escape during breast carcinoma progression.

  PMID 41997138 · PMC13213619 · Cancer cell · 2026 · 8 claims · 8 setups

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  A novel proliferative Treg precursor state, cycling Treg (cycTreg: FOXP3^int, MKI67^hi, IKZF2/4^int-hi), is absent in normal breast, low in DCIS, and strongly expanded in IBC

  normal mammary dcis tumor-draining scrna-seq spatial multiplex

• SPP1(+) macrophage-driven interactions shape the tumor microenvironment in lymph node metastatic acral melanoma.

  PMID 42020397 · PMC13230793 · Cell death & disease · 2026 · 8 claims · 8 setups

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  LN+ acral melanoma shows preferential SPP1+ signaling, including autocrine amplification within SPP1+ macrophages and paracrine interaction with S100A8+ melanoma cells via the SPP1-CD44 axis

  tumor microarray thp-1 a375 scrna-seq immunofluorescence western

• Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

  PMID 42058918 · PMC13123497 · iScience · 2026 · 7 claims · 6 setups

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  Fibroblast culture leads to subtype assimilation, with in vivo heterogeneity persisting only minimally by passage 4

  dermal mesenchymal stromal patient-matched single-cell bulk qpcr

• Agent-based modeling of cellular dynamics in adoptive cell therapy.

  PMID 41673469 · PMC13004971 · Communications biology · 2026 · 7 claims · 7 setups

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  ABMACT, an agent-based model of adoptive cell therapy, recapitulated cellular dynamics in two cancer preclinical models (lymphoma and glioblastoma mouse models).

  xenograft il-15-armored cord shanley scrna-seq autonomous rechallenge

• Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

  PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  COL6A3+ TAFs are a distinct matrix-fibroblast subset significantly enriched in non-responders to neoadjuvant antiangiogenic+ICB combination therapy

  gbm ffpe col6a3+ thp-1 scrna-seq spatial multiplex

• GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

  PMID 40204713 · PMC11982250 · Nature communications · 2025 · 8 claims · 7 setups

  Has reproduction · 91

  GRAMD1B is increased in excitatory neurons of human neural organoids (HNOs) carrying the MAPT R406W mutation

  neural hno single-cell immunofluorescence western

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence