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).

Publications 1.3k Datasets 392.5k Experiments 49

Assay: tgf-β ✕ Clear

Tenascin C(+) myofibroblasts exacerbate vascular neointimal hyperplasia by propagation of nerve-macrophage interactions in mice.

PMID 41617709 · PMC12960667 · Nature communications · 2026 · 7 claims · 8 setups

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A distinct population of Tnc+ myofibroblasts (cluster iFb5) emerges from adventitial fibroblasts during ligation-induced neointimal hyperplasia

carotid adventitial pdgfrα nih-3t3 scrna-seq spatial immunofluorescence
Innate antiviral and immune functions associated with the HIV reservoir decay after anti-PD-1 therapy.

PMID 41680482 · PMC12920136 · Nature medicine · 2026 · 7 claims · 7 setups

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Anti-PD-1 therapy triggers a rapid (within 24 hours) systemic cascade of increased IFN/antiviral, monocyte, and CD8+ T cell effector transcriptomic modules alongside decreased plasma TGFβ.

pbmcs plasma pbmc publicly bulk plasma integrated
Monocytes Defined by Platelet Interactions and Oxidative Stress Signaling Underlie HIV-Associated Atherosclerosis.

PMID 41823228 · PMC13055746 · Journal of the American Heart Association · 2026 · 8 claims · 8 setups

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Two monocyte clusters (platelet-monocyte complex [PMC] and CD14+ monocytes) contribute independently to vascular immune dysregulation in PLWH

circulating plasma platelet-monocyte cd14+ single-cell plasma bulk
EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets.

PMID 42097304 · PMC13186194 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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EMTscore is an R package providing efficient, unbiased scoring of multiple EMT pathways from single-cell or bulk omics data

small a549 trunk bulk scrna-seq
Signals controlling neural crest contributions to the heart.

PMID 20490374 · PMC2873602 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 8 setups

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Semaphorin3C (from outflow myocardium) signals through PlexinA2 (on neural crest) to guide cardiac neural crest migration into the outflow tract

sema3c chick cardiac genetic pharmacologic conditional
Predicting position along a looping immune response trajectory.

PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 6 setups

Has reproduction · 98

Looper is a computational method that automatically identifies phase-shifted gene pairs (using SAX symbolic representation) that trace loops in longitudinal expression data.

monocytes blood pbmcs montreal microarray qrt-pcr topological
Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

Has reproduction · 100

The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

bulk py2t mcf10a airway transcriptomic rna-seq single-cell
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

hepatocellular p53 genomic hepatoma array-based pooled shrna
Mercury immune toxicity in harbour seals: links to in vitro toxicity.

PMID 18959786 · PMC2600635 · Environmental health : a global access science source · 2008 · 8 claims · 6 setups

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In vitro MeHg exposure reduces seal lymphocyte number, viability, metabolic activity, and DNA/RNA synthesis

blood pha-stimulated cytoplasmic cold trypan mts
HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

PMID 18849997 · PMC3334282 · Nature medicine · 2008 · 8 claims · 8 setups

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HIT uses oligonucleotide-tagged (Fab- or mSA-conjugated) antibodies, T7 polymerase amplification, and DNA microarray hybridization to indirectly measure multiple analytes in a fluid-phase multiplex format

hsp70-coated hsp70 secreted jurkat fluid-phase multiplex hit
Stemming cancer: functional genomics of cancer stem cells in solid tumors.

PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

solid fetal cd133+ breast facs neurosphere genome-wide
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
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
Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

PMID 41574606 · PMC12892883 · JCI insight · 2026 · 8 claims · 8 setups

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Chondrocyte-specific (Col2a1-Cre-driven) expression of the p.R594H Trpv4 mutation reproduces the human TRPV4 skeletal dysplasia phenotype in mice, including short stature, long bone and craniofacial abnormalities, and vertebral defects.

col2a1-cre proximal growth cervical radiography histology rnascope
Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

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snRNA-seq census of 227,680 nuclei across 48 cell types reveals altered cellular states and compositional rewiring of the distal lung in ILD

frozen lung flash-frozen spatial single-nucleus scrna-seq 10x
Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

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Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

dissected same tumor xenium-derived bulk enzymatic whole-genome
Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

PMID 41618002 · PMC12960917 · Communications biology · 2026 · 8 claims · 8 setups

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Murine tumor pericytes originate from normal tissue-resident pericytes that proliferate inside tumors

aom crc pdgfrβ-creert2 notch3-creert2 scrna-seq facs lineage
Maternal Fine Particulate Matter Exposure Impairs Inguinal White Adipose Tissue Plasticity in Middle-Aged Male Mouse Offspring.

PMID 41648986 · PMC12918713 · ACS nano · 2026 · 7 claims · 8 setups

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Maternal PM2.5 exposure induces insulin resistance in middle-aged male (but not female) offspring despite normal body weight/obesity status

pregnant iwat adsc whole-body body histology
CD38 expression by neonatal human naive CD4+ T cells shapes their distinct metabolic and tolerogenic properties.

PMID 41746743 · PMC13078883 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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CD38 is markedly more highly expressed on cord blood (CB) naive CD4+ T cells than adult blood (AB) naive CD4+ T cells, with an age-dependent gradient from fetal to pediatric life.

pbmcs sorted scrna-seq naive flow bulk compass
Autocrine SFRP2 (secreted frizzled related protein 2) enhances lung myofibroblast fibrogenic activity by suppressing PINK1-mediated mitophagy initiation.

PMID 41789512 · PMC13185440 · Autophagy · 2026 · 7 claims · 8 setups

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SFRP2 is specifically highly expressed in myofibroblasts derived from fibrotic (IPF/BLM/TGFB1-induced) lung tissue

lung pmlfs mrc5 single-cell bulk histology

Experiments

Tenascin C(+) myofibroblasts exacerbate vascular neointimal hyperplasia by propagation of nerve-macrophage interactions in mice.

Innate antiviral and immune functions associated with the HIV reservoir decay after anti-PD-1 therapy.

Monocytes Defined by Platelet Interactions and Oxidative Stress Signaling Underlie HIV-Associated Atherosclerosis.

EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets.

Signals controlling neural crest contributions to the heart.

Predicting position along a looping immune response trajectory.

Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

Mercury immune toxicity in harbour seals: links to in vitro toxicity.

HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

Stemming cancer: functional genomics of cancer stem cells in solid tumors.

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

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

Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

Maternal Fine Particulate Matter Exposure Impairs Inguinal White Adipose Tissue Plasticity in Middle-Aged Male Mouse Offspring.

CD38 expression by neonatal human naive CD4+ T cells shapes their distinct metabolic and tolerogenic properties.

Autocrine SFRP2 (secreted frizzled related protein 2) enhances lung myofibroblast fibrogenic activity by suppressing PINK1-mediated mitophagy initiation.