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).

• Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.

  PMID 42024616 · PMC13188987 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  MUSTARD is a trajectory-guided dimensionality reduction method for multi-sample, multi-condition scRNA-seq data that simultaneously captures gene expression variation along pseudotime and across samples

  simulated covid-su covid-stephenson tuberculosis data-driven scrna-seq pseudobulk-pca

• Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

  PMID 42025535 · PMC13105851 · Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026 · 8 claims · 8 setups

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  A pediatric single-cell PBMC reference atlas was developed from 57 healthy children across 8 public scRNA-seq studies.

  pbmcs cd3+ cd4+ memory scrna-seq pseudobulk bulk

• Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

  PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical

  intestine rodent duodenal neonatal bulk scrna-seq marker

• 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

• 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

• 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

• Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

  PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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  Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

  pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised

• 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

• 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

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 7 setups

  Has reproduction · 100

  A novel computational (Snakemake) pipeline quantifies intratumoral heterogeneity in MSI status at single-cell resolution

  colorectal cancer aggregated msisensor-rna single-cell cnv-based

• 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

• 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

• Clonal CD8(+) T cells populate the leptomeninges and coordinate with immune cells in human degenerative brain diseases.

  PMID 41593242 · PMC12864034 · Nature immunology · 2026 · 8 claims · 6 setups

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  The human leptomeninges harbor substantial numbers of clonally expanded, tissue-resident memory CD8 T cells (ZNF683-high, CXCR6+, PD-1+)

  postmortem leptomeninges scrna-seq-derived leptomeningeal single-cell flow imaging

• 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

• Single-cell atlas of the developing Down syndrome brain cortex.

  PMID 41545595 · PMC13004680 · Nature medicine · 2026 · 8 claims · 8 setups

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  RORB/FOXP1-expressing L4-like excitatory neurons are subtype-specifically and dramatically reduced in Down syndrome fetal cortex, especially at later stages (PCW16-20)

  fetal excitatory neural humanized single-nucleus immunostaining compositional

• 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

• Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR.

  PMID 41771837 · PMC12953643 · Signal transduction and targeted therapy · 2026 · 8 claims · 8 setups

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  KLF15 transcriptional activity shows the most significant change among TFs in pathological cardiomyocytes during progressive hypertrophic remodeling, reflecting less effective repression of disease-associated genes.

  ventricular heart cardiomyocytes cardiomyocyte single-cell rt-qpcr bulk

• 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

• 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