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).

• Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

  PMID 40874534 · PMC12808545 · Biology of reproduction · 2026 · 6 claims · 6 setups

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  IVF-conceived mouse placentae exhibit global and cell type–specific gene expression differences compared to FB placentae

  e12.5 differentially trophoblast placenta single-nucleus pseudobulk pathway

• High-quality acinar cell isolation enables single-cell analysis of healthy and injured pancreas.

  PMID 42013858 · PMC13198085 · Cell reports methods · 2026 · 8 claims · 7 setups

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  The DCTC protocol isolates up to 90% acinar cells from healthy wild-type pancreatic tissue without cell fixation or dead-cell removal kits

  healthy pancreas epithelial kpc scrna-seq pseudobulk velocity

• Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

  PMID 41729083 · PMC12956012 · JCI insight · 2026 · 8 claims · 7 setups

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  A clonally expanded CD8+GZMK+IFNG+ T cell population (subdivided into IFNGhi and IFNGint groups) is enriched in the EM lesion and shows an inflammatory, tissue-resident phenotype (GZMBlo/PRF1-) resembling tissue-enriched GZMK+ TteK cells

  whole-skin cd8+gzmk+ifnghi identified skin scrna-seq pseudobulk immune

• Cellular insights into transposable elements in Alzheimer's disease.

  PMID 41573740 · PMC12819740 · Frontiers in molecular biosciences · 2025 · 8 claims · 5 setups

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  508 TE loci are differentially expressed in AD brain, with the large majority (84.3%) upregulated, indicating widespread TE activation

  postmortem brain genome genes single-nucleus atac-seq pseudobulk

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

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

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  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

• Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

  PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

  postmortem million+ pfc each single-nucleus umap pseudobulk

• 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

• Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

  PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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  Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

  substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell

• Single-cell transcriptomics identifies regulatory T cell heterogeneity in gestational diabetes mellitus.

  PMID 41933176 · PMC13223204 · Communications medicine · 2026 · 8 claims · 8 setups

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  Treg cluster proportions do not significantly differ between GDM and healthy control patients

  sorted pbmcs treg gdm-patient single-cell mass gene

• Single-cell spatiotemporal dissection of the human maternal-fetal interface.

  PMID 41951740 · PMC13149032 · Nature · 2026 · 8 claims · 8 setups

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  Generated a comprehensive single-cell multiomic and spatial atlas of the human maternal-fetal interface from early gestation to term

  decidua maternal-fetal pseudobulk trophoblast paired genotype snatac-seq

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

  liver mm39 bulk single-nuclei ahr

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Ion-Channel-Mediated Drug Repurposing Opportunities Validated by Single-Cell Perturbation in Colorectal Cancer.

  PMID 42074061 · PMC13116841 · International journal of molecular sciences · 2026 · 8 claims · 6 setups

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  WGCNA on CRC transcriptomes identified 100 hub genes spanning three functional programs: ribosomal biogenesis, RNA processing, and immune

  crc independent hct116 bulk protein-protein vgae-based