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).

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

  PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

  nsclc epithelial macrophage caf scrna-seq copy gene-set

• SpaJoint: a transfer learning method for spatial transcriptomics deconvolution.

  PMID 41955028 · PMC13069903 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

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  SpaJoint is a transfer-learning-based deconvolution method that integrates scRNA-seq and ST gene expression while accounting for spatial correlation across spots.

  simulated spatial

• Tumour-intrinsic features shape T cell differentiation through precursor to symptomatic multiple myeloma.

  PMID 41644568 · PMC12982522 · Nature communications · 2026 · 8 claims · 6 setups

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  MM is not characterized by T cell exhaustion but by antigen-driven terminal memory differentiation, unlike solid cancers

  bone cd69+ cd8+ smm single-cell cite-seq gene

• A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing.

  PMID 38839790 · PMC11153528 · Scientific data · 2024 · 8 claims · 4 setups

  Has reproduction · 95

  Established a protocol for isolating single cells from Ae. aegypti midgut and performing scRNA-seq (dissociation, density-gradient purification, viability QC, 10x Genomics library prep and sequencing).

  dissociated scrna-seq merged single-cell viability computational

• Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability.

  PMID 41949281 · PMC13061419 · eLife · 2026 · 7 claims · 6 setups

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  Human marker genes are less effective in macaques and vice versa, showing limited transferability of markers across species.

  ipsc-derived day integrated ipscs scrna-seq flow immunofluorescence

• Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

  PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

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  ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

  acl differentially study flow single-cell immunofluorescence

• Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.

  PMID 41710887 · PMC12909565 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  Higher EZH2 expression is associated with adverse clinical outcomes in bulk PCa/CRPC cohorts

  tcga-prad su2c gse264573 gse137829 bulk scrna-seq ligand-receptor

• Generation of thymus-reconstituting T cell progenitors from human pluripotent stem cells.

  PMID 41512861 · PMC12853186 · Cell reports methods · 2026 · 7 claims · 6 setups

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  A cytokine-free hPSC hematopoietic differentiation protocol followed by OP9-DLL4 stromal co-culture generates pro-T cells without genetic manipulation

  hpsc hescs hpsc-hec-derived sorted flow tcr single-cell

• 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

• Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair.

  PMID 41617708 · PMC12960685 · Nature communications · 2026 · 8 claims · 8 setups

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  A genetically engineered mouse model (Krt14-CreER; LSL-rtTA-EGFP; TetO-OSKM-mCherry, 'Epi-iOSKM') enables transient, reversible, mosaic OSKM expression in interfollicular epidermal cells without inducing pluripotency or teratoma risk

  epidermis sorted epidermal ife immunostaining single-cell pseudotime

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Spatial cartography of human thymus enables the geopositioning of lineage transcription factors in rare mimetic thymic epithelial cells.

  PMID 41807357 · PMC13102919 · Nature communications · 2026 · 7 claims · 7 setups

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  Generated a high-resolution spatial transcriptomic atlas of human fetal (13,14,17,18w) and paediatric (7w,2y,5y,6y) thymi using Stereo-seq, integrated with scRNA-seq and MACSima/Stereo-CITE proteomics

  fetal paediatric thymus stereo-seq scrna-seq macsima

• Chemotherapy-induced reactive myelopoiesis promotes expansion of immunosuppressive neutrophil-like monocytes in mice and humans.

  PMID 41945895 · PMC13232731 · JCI insight · 2026 · 8 claims · 8 setups

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  Monocytes from lymphoma patients receiving CTX-containing chemotherapy show variable, often chemotherapy-induced or -enhanced, immunosuppressive activity against T cells

  pbmcs bone sorted facs-sorted scrna-seq flow atac-seq

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

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  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

  PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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  The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

  first-trimester decidual spots dnk 10x h&e type

• 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

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime