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).

• 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

• 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

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 6 setups

  Has reproduction

  D2H2 is a web-based portal integrating hundreds of curated diabetes-relevant transcriptomics datasets with bioinformatics tools for gene/gene set queries

  brain top curated d2h2 differential gene bulk

• 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

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 90

  Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

  sural peripheral snrna-seq nerve single-nucleus subcellular situ

• 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 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

• 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

• 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

• pmid-41573740

  PMID 41573740 · PMC12819740 · 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

• Single-cell resolution of an open chromatin signature in persister tumor cells.

  PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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  Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

  non-malignant same epithelial tumor single-nucleus mitochondrial copy-number

• sCellST predicts single-cell gene expression from H& E images.

  PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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  sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

  ovarian kidney prostate breast simulation spot-level nucleus

• Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

  PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

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  snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

  ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence

• 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-41576947

  PMID 41576947 · PMC12985369 · 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

• 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

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

  PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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  Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

  individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched