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

• 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 nuclei and spatial profiling of sacrococcygeal teratomas reveals cellular composition and X inactivation heterogeneity.

  PMID 41565739 · PMC12949016 · NPJ precision oncology · 2026 · 7 claims · 4 setups

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  snRNA-seq and spatial transcriptomics of eight SCTs identify five broad cell lineages (neuroectoderm, epithelia, stroma, endothelia, immune) resolved into 26 transcriptionally distinct subtypes

  postnatal prenatal aggregated single-nucleus single-cell spatial

• pmid-41571662

  PMID 41571662 · PMC12923738 · 8 claims · 8 setups

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  Fin and limb regeneration share conserved proximal and distal blastema territory markers, DNA damage repair activation, hif1a-mediated hypoxia response, and sequential pro-/anti-inflammatory gene programs.

  polypterus axolotl zebrafish regenerating single-nucleus spatial single-cell

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

  patient-derived tumor single paired single-nucleus infercnv aracne-ap

• Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

  PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

  snscc bulk single-nucleus bulk single-nucleus methylation

• Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

  PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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  MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

  microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus

• Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

  PMID 41111196 · PMC12506984 · Hepatology communications · 2025 · 8 claims · 3 setups

  Has reproduction · 77

  2D culturing of primary hepatocytes for 24 hours causes extensive transcriptomic (>10,000 genes) and proteomic (>3000 proteins) rewiring compared with freshly isolated cells

  c57bl same bulk quantitative single-nucleus

• Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

  PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

  pancreatic kpc pdac tcga-paad rna-seq bulk proteomics

• Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.

  PMID 41370097 · PMC12807774 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Expression Atlas has expanded to >4500 studies from 67 species, with increased proteomics coverage and updated GTEx tissue profiles

  species pig tissues gtex microarray bulk ms-based

• Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

  PMID 41746809 · PMC13042203 · Cell reports · 2026 · 8 claims · 8 setups

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  UPF2-mediated NMD is required for proper cortical lamination; conditional Upf2 deletion in radial glia disrupts layering of TBR1+/SATB2+ and CTIP2+/CUX1+ neurons.

  cortex embryonic cortical neural immunofluorescence utero co-electroporation

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.

  PMID 41258799 · PMC12862343 · Cancer research · 2026 · 8 claims · 6 setups

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  Serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female patients with PDAC than in male patients

  pdac pdx magnetic bioinformatic single-nucleus

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

  PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

  fresh matched archived dsrct scrna-seq single-nucleus bulk

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western