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).

• 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

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

  PMID 41666923 · PMC12923953 · Cell reports. Medicine · 2026 · 8 claims · 5 setups

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  Tumors stratify into lymphoid-enriched, myeloid-enriched, and mixed immune-infiltrated subtypes independent of oncogenic driver status

  resected luad cd4+ multiplex spatial image

• A human tumor-immune organoid model of glioblastoma.

  PMID 41505256 · PMC12969483 · Cell reports · 2026 · 8 claims · 8 setups

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  iHOTT is an autologous co-culture platform integrating patient-derived tumor cells and matched PBMCs within human cortical organoids

  ihott sorted recurrent flow immunostaining multiplex

• Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.

  PMID 41660271 · PMC12876322 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  A 9-gene Immune-Chemotherapy Prediction Score (ICPscore), derived from ORIENT-11 via WGCNA and LASSO Cox regression, predicts survival benefit from ICI plus chemotherapy in advanced NSCLC

  orient-11 hub nsclc oak bulk pd-l1 wgcna

• Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

  PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

  csf peripheral brain cell-free single-cell deep spatial

• Comparative single-cell landscape of immune cells in human livers affected HBV and non-viral cirrhosis.

  PMID 41815278 · PMC12971635 · Frontiers in medicine · 2025 · 8 claims · 7 setups

  Full-text index only

  Macrophage-PLCG2 (anti-inflammatory) and CD8+ T-FABP5 subsets are expanded in HBV cirrhosis compared to non-viral cirrhosis

  liver myeloid scrna-seq spatial pathway

• Predictive modeling of molecular activity underlying physical cell-cell interactions.

  PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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  Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

  tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq

• Reciprocal regulation of fibroblast-macrophage equilibrium governs skin integrity.

  PMID 41760904 · PMC13043295 · Nature immunology · 2026 · 8 claims · 8 setups

  Full-text index only

  Dpt+ fibroblasts are required to maintain skin macrophage populations in vivo; their depletion reduces CD64+ and CD11c+ macrophages

  facs-sorted skin dpt+ scrna-seq flow cellchat

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• Host-derived interleukin-1α drives tumor immunosuppression by reprogramming tumor-associated myeloid cells.

  PMID 41547846 · PMC12910057 · NPJ breast cancer · 2026 · 8 claims · 8 setups

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  Deletion of host Il1α causes rejection/regression of transplanted breast tumors

  h605 pymt tumor-infiltrating two-week orthotopic flow single-cell

• Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

  PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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  Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

  hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Identification of novel DNA sequence motifs that modulate transcription in T cells.

  PMID 41514212 · PMC12879379 · BMC genomics · 2026 · 8 claims · 8 setups

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  Identified 2,036 novel DNA motifs enriched in regulatory regions of T-cell-specific genes

  t-cell non-t-cell cd4+ sequences rna-seq dnase-seq h3k27ac

• POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

  PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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  Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

  hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry

• GATA2 controls alveolar macrophage inflammatory gene expression and metabolic function.

  PMID 41712459 · PMC13134736 · JCI insight · 2026 · 8 claims · 8 setups

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  GATA2 deficiency promotes enhanced inflammatory gene expression and metabolic dysfunction in alveolar macrophages in response to type 2 stimuli

  bal cd11c+ ams lung flow immunostaining bodipy

• Airway injury induces alveolar epithelial responses mediated by macrophages.

  PMID 41579370 · PMC13090803 · Cell reports · 2026 · 8 claims · 8 setups

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  Club cell injury (naphthalene) induces transient proliferation of distal AT2 progenitor cells

  lung bronchoalveolar club alveolar-enriched single-cell immunofluorescence flow

• 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

• Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment.

  PMID 41817317 · PMC13223553 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 8 claims · 7 setups

  Full-text index only

  High-grade histopathologic TIL infiltration is associated with significantly prolonged overall survival in breast and lung cancer BM.

  breast lung histopathologic sequencing tcr

• Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

  PMID 41623476 · PMC12857400 · iScience · 2026 · 7 claims · 12 setups

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  Splicing-modulatory drugs MS023 and indisulam act as inadvertent NMD inhibitors by downregulating SMG1 protein levels

  4t1 tumor-draining arst panc02 mts tumor ifn-γ