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).

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

  PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

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  Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

  trp53-null complete t12 cell-deficient imaging survival tumor

• 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

• Sequential RNA polymerase II activation drives human hematopoiesis.

  PMID 41520338 · PMC13067999 · Cell reports · 2026 · 7 claims · 7 setups

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  sciCUT&Tag2in1 enables simultaneous single-cell combinatorial-indexing profiling of Pol II occupancy (Ser5/Ser2-phospho CTD) together with histone modifications (H3K4me1-2-3 or H3K27me3) in up to 50,000 cells per experiment

  g-csf-mobilized cd34+ 10-donor lineage-depleted scicut&tag2in1 individual souporcell

• 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

• 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 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

• A ligand-centered framework for γδ T cell activation in colorectal cancer revealed by single-cell and transformer-based perturbation.

  PMID 41607803 · PMC12835328 · Frontiers in immunology · 2025 · 8 claims · 8 setups

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  CRC-infiltrating γδ T cells show varied activation levels, with the TRM-like population being the major tumor-infiltrating subtype and exhibiting the lowest effector and exhaustion signature scores.

  crc-infiltrating crc scrna-seq gene nichenet

• Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

  PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups

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  446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways

  carotid degs six bulk kegg logistic

• 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

• The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

  PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

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  EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

  ehf facs-sorted dss-induced lethal cd4+

• Cardiac conduction system malformations in heterotaxy result from dysregulated Pitx2 expression.

  PMID 41734036 · PMC13043103 · JCI insight · 2026 · 8 claims · 8 setups

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  Cryptic-/- embryos (right isomerism model) develop bilateral sinoatrial nodes and an ectopic anterior AV node and bundle, accompanied by reduced Pitx2 expression

  cryptic embryo pitx2 lefty1 situ immunostaining cardiac

• Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

  PMID 41758930 · PMC13197979 · Blood · 2026 · 8 claims · 6 setups

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  Orca-T immunotherapy leads to increased phenotypic T-cell activation compared with unmanipulated PBSC grafts, persisting for months after treatment.

  peripheral sorted fresh cryopreserved flow single-cell tcr

• 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

• Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

  PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

  Has reproduction · 74

  Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

  peripheral rna-seq flow edu antibody