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 P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

  PMID 41559646 · PMC12910786 · BMC cancer · 2026 · 6 claims · 8 setups

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  A tumor cell metaprogram (MP7) identified from scRNA-seq of CSCC shows elevated hypoxia, invasion, metastasis, proliferation, and angiogenesis scores compared to other metaprograms.

  cscc tcga-cscc mp7 siha single-cell bulk gene

• 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

• Tissue-resident macrophage and dendritic cells drive type I IFN immunity to enteroviruses in the liver.

  PMID 41592119 · PMC12858076 · PLoS pathogens · 2026 · 8 claims · 6 setups

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  Type I IFN signaling (Ifnar1), but not type III IFN signaling (Ifnlr1), is essential for survival and for limiting viral replication in the liver during echovirus infection

  neonatal liver survival viral h&e

• 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

• 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

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

  PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

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  SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

  pbmc bone skin embryos scrna-seq scnmt-seq asap-seq

• TriticeaeExpDB: a centralized transcriptomic resource for Triticeae research.

  PMID 41656232 · PMC12983667 · BMC genomics · 2026 · 8 claims · 8 setups

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  TriticeaeExpDB integrates and uniformly reprocesses >10,000 (11,016) RNA-seq samples from 528 BioProjects/studies across 17 Triticeae species

  triticeae rna-seq user-selected user-supplied bulk biological differential

• Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

  PMID 41664205 · PMC12990480 · Genome biology · 2026 · 8 claims · 8 setups

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  Developed an improved protoplasting/hand-picking protocol enabling isolation of intact QC cells for single-cell long-read RNA sequencing (SCAN-seq)

  arabidopsis single-cell rt-pcr agarose

• Multiomics combined drugs to explore the potential mechanism and treatment of ankylosing spondylitis.

  PMID 41673882 · PMC13047816 · Journal of orthopaedic surgery and research · 2026 · 8 claims · 8 setups

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  Effector CD8+ memory T (Tem) cells are significantly elevated in AS patients compared to healthy controls

  bone peripheral effector interspinous single-cell cibersortx cell-cell

• Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells.

  PMID 41677588 · PMC12896614 · Cells · 2026 · 8 claims · 6 setups

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  Alternative splicing of IKZF1 in human T cells strongly influences gene expression, chromatin accessibility, and protein production.

  jurkat genomic cd4+ rna-seq atac-seq immunoblotting

• Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.

  PMID 41688638 · PMC12987725 · Nature genetics · 2026 · 8 claims · 8 setups

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  Variants in the OR51E1–OR51E2 locus, encoding microbiome-derived fatty acid chemosensors expressed in enteroendocrine cells, are associated with gut microbial richness

  adults subset intestinal enteroendocrine genome-wide sanger single-cell

• Lactate metabolism-related interaction perturbation network enables robust stratification of hepatocellular carcinoma.

  PMID 41689750 · PMC13009326 · Discover oncology · 2026 · 8 claims · 8 setups

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  An LM-related gene interaction perturbation network can stratify HCC into four robust molecular subtypes (Cluster1-4)

  tcga-hcc gse76427 gene consensus 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

• CRISPR-based functional genomics for dissecting therapeutic dependency in primary acute myeloid leukemia samples.

  PMID 41759529 · PMC13036604 · Molecular cell · 2026 · 8 claims · 8 setups

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  An optimized dual-lentiviral CRISPR-Cas9 knockout system with fluorescent markers, SFFV promoter, and improved sgRNA backbone (LRG2.1) achieves efficient, low-toxicity gene editing in AML PDX and primary patient samples

  aml pdx#2263 molm-13 pdx#062614 crispr pooled domain-focused

• IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

  PMID 41766654 · PMC12948414 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  MPNST cells are more radioresistant than benign plexiform neurofibroma (pNF) cells in vitro

  mpnst st88-14 nf9511.b jh-2-002 flow fractionated bulk

• Colonic Engyodontium fungus triggers neutrophil antimicrobial activity to suppress Lactobacillus johnsonii-derived glutamic acid-maintained Tregs.

  PMID 41770903 · PMC13078882 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  A commensal Ascomycota fungus, Engyodontium sp., was isolated live from mouse feces using a Dectin-2-Fc fusion protein

  feces colonic colon ncm460 its flow qpcr

• Integrative omics and experimental validation reveal METTL17 and SLC27A1 as biomarkers and potential therapeutic targets in chronic kidney disease.

  PMID 41766913 · PMC12946038 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  METTL17 and SLC27A1 are identified as consistently dysregulated key genes bridging mitochondrial dysfunction and macrophage polarization in CKD

  kidney peripheral uuo bulk single-cell cibersort

• Targeting the Lipid Metabolism Proteins FASN and GPAM in Alveolar Type II Cells Decreases Lung Metastasis.

  PMID 41778850 · PMC7619144 · Cancer discovery · 2026 · 7 claims · 8 setups

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  AT2 cells and surfactant lipids (e.g., PC, PE, PI, PG) are enriched in the vicinity of breast cancer lung metastases in both patients and mice

  postmortem lungs lung at2 immunohistochemistry maldi-msi longitudinal

• Matcha alleviates sneezing response in a murine model of allergic rhinitis.

  PMID 41786771 · PMC13022397 · NPJ science of food · 2026 · 8 claims · 8 setups

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  Matcha suppresses allergen-induced immediate nasal response (INR) and nasal hyperresponsiveness (NHR) in an OVA-immunized mouse model

  balb fecal cd4+ expanded sneeze nasal serum