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 41

System / cell line: wound ✕ Assay: wound ✕ Clear

Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.

PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups

Has reproduction · 68

Chronic wound-edge tissue shows genome-wide DNA hypermethylation compared with unwounded skin

chronic wound-edge unwounded ischemic whole-genome bisulfite bulk
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.

PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups

Has reproduction · 78

A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin

injured normal p2-whgs oral bulk single-cell gene
A macrophage-induced subpopulation of mesenchymal cells expressing Fcer1g contributes to wound-induced fibrosis.

PMID 41680182 · PMC13009336 · Nature communications · 2026 · 8 claims · 7 setups

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Early-phase macrophage depletion (MaFIA + AP20187) reduces fibrosis/scar area and mesenchymal cell numbers without delaying reepithelialization or angiogenesis.

mafia nih pdgfra-rtta flow excisional immunofluorescence
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

Has reproduction · 78

In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

aeruginosa differentially paired rna-seq tn-seq computational
Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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VLU infections are polymicrobial with no single bacterium colonizing the wounds

individual pooled second btefap quantitative bulk
Advanced Glycation End-Products Contribute to Delayed Diabetic Corneal Epithelial Wound Healing via the TLR4 Signaling.

PMID 41718657 · PMC12927432 · Investigative ophthalmology & visual science · 2026 · 8 claims · 8 setups

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AGE accumulation is significantly increased in diabetic corneas compared to normal corneas

bmdcs bmdc corneal t1dm sequencing western quantitative
Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor.

PMID 41931622 · PMC13048245 · Science advances · 2026 · 7 claims · 8 setups

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Brain-specific (neural crest-derived, NC-SMC) but not peripheral (LPM-SMC/PM-SMC) iPSC-derived VSMCs are selectively vulnerable to CADASIL NOTCH3 variants

ipsc-derived ivsmcs immunofluorescence wound collagen
Sensitizer-Induced Basophils Accelerate Skin Re-Epithelialization via IL-4/IL-13-Mediated Macrophage Polarization.

PMID 41787818 · PMC13139821 · Allergy · 2026 · 8 claims · 8 setups

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Basophils accumulate in wounded and oxazolone (OXA)-sensitized skin, peaking around day 3–6 post-injury

skin ear dorsal mcpt8-ct single-cell flow rt-qpcr
IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

PMID 41559031 · PMC12819398 · Cell discovery · 2026 · 8 claims · 8 setups

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Aging reduces hASC self-renewal, lineage plasticity (adipogenic/osteogenic differentiation), and in vivo tissue repair efficacy

i-hascs full-thickness nude hascs edu scratch adipogenic
Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

PMID 33779545 · PMC8049744 · eLife · 2021 · 8 claims · 5 setups

Has reproduction · 100

The initial transcriptional response to amputation is identical during head and foot regeneration at 3 hpa

hydra atac-seq rna-seq chromvar
Interpretation of genomic data: questions and answers.

PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

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The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

genetically wound tumor breast gene expression comparative
Agonal cell resuscitation strategy to promote tissue repair.

PMID 41965918 · PMC13246746 · Nature communications · 2026 · 8 claims · 8 setups

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Agonal cells upregulate endocytosis and SNARE-mediated vesicular transport machinery and phosphatidylserine receptor (PSR) genes, enhancing uptake of extracellular vesicles (EVs)

ripk3-oe six wound hmlkl bulk single-cell flow
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr
Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

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scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

umbilical porcine puvec histology immunostaining real-time
Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

PMID 41484106 · PMC12881549 · Nature communications · 2026 · 8 claims · 8 setups

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Loss/inhibition of IKKα unexpectedly promotes, rather than suppresses, CRC liver metastasis in patient-derived organoid (PDO) xenograft models.

pdo5 pdo5-derived crc dld1 intrasplenic immunohistochemistry kaplan-meier
Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

PMID 41562071 · PMC12813044 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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GDPD3 is upregulated in PRAD tumor tissue and its knockdown inhibits tumor cell proliferation, invasion, and migration

prad tcga-prad du145 scrna-seq bulk wgcna
Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

pca tcga-prad external scrna-seq bulk immune
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

skin combined annotated scrna-seq single-cell spatial cell2location
Single-cell transcriptomic analyses reveal angiogenic vascular responses to chronic cerebral hypoperfusion.

PMID 41907427 · PMC13019947 · iScience · 2026 · 8 claims · 8 setups

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A distinct endothelial tip cell subcluster emerges and expands in the brain after chronic cerebral hypoperfusion (ACAS)

brain mbmec acas single-cell laser immunostaining
Multiomic and functional validation of ACSL3, a regulator of fatty acid metabolism, as a lymph node metastasis-associated gene in lung adenocarcinoma.

PMID 41998631 · PMC13261843 · Respiratory research · 2026 · 8 claims · 8 setups

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A five-gene FAM-related risk signature (ACSL3, MCAT, NDUFAB1, OLAH, ACSL4)-derived FScore stratifies LUAD prognosis across multiple independent cohorts

tcga-luad luad a549 lymphatic bulk scrna-seq spatial

Experiments

Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.

SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.

A macrophage-induced subpopulation of mesenchymal cells expressing Fcer1g contributes to wound-induced fibrosis.

Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

Advanced Glycation End-Products Contribute to Delayed Diabetic Corneal Epithelial Wound Healing via the TLR4 Signaling.

Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor.

Sensitizer-Induced Basophils Accelerate Skin Re-Epithelialization via IL-4/IL-13-Mediated Macrophage Polarization.

IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

Interpretation of genomic data: questions and answers.

Agonal cell resuscitation strategy to promote tissue repair.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

Single-cell transcriptomic analyses reveal angiogenic vascular responses to chronic cerebral hypoperfusion.

Multiomic and functional validation of ACSL3, a regulator of fatty acid metabolism, as a lymph node metastasis-associated gene in lung adenocarcinoma.