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).

• 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

• Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

  PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

  Full-text index only

  Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

  drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic

• Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

  PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

  Full-text index only

  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

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence With Existing Human Data.

  PMID 41566898 · PMC12824456 · Brain and behavior · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  A meta-analysis of 6 public PFC transcriptional profiling datasets (n=117 mice, 8 stress vs control contrasts) identified 133 genes consistently differentially expressed across chronic stress studies and paradigms (FDR<0.05)

  c57 c57bl post-weaning pooled microarray rna-seq random-effects

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• UBE2M as a bridge spanning neddylation and cell cycle regulation in colorectal adenocarcinoma.

  PMID 41680469 · PMC12993059 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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  Neddylation is associated with G2M phase progression in CRC

  crc paired hek293t cell-free single-cell bulk immunohistochemistry

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A 279-gene 'iMSC signature' is upregulated in BM MSCs from MM patients compared to healthy donors, identified by reanalysis of single-cell RNA-seq data.

  facs-isolated expanded bm-mscs mscs single-cell bulk gene

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• 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 multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis.

  PMID 41862476 · PMC13004862 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  Mechanical stress (MS) signaling is significantly elevated in endothelial cells (ECs) from IPF patients and correlates with fibrosis severity and lung function decline

  lung cd31+ single-nucleus scissor meta-analysis

• Protocol for single-cell optimization objective and trade-off inference.

  PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups

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  SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs

  mcf10a serum-starved contact-inhibited zygote bulk scrna-seq genome-scale

• Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation.

  PMID 41477881 · PMC12850507 · Science (New York, N.Y.) · 2026 · 8 claims · 8 setups

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  A haplotype at the 17q22 locus, tagged by the noncoding variant rs17834140-T, is a causal protective variant against CHIP and myeloid malignancies

  population hspcs cd34+cd45ra-cd90+ heterozygous gwas atac-seq crispr

• DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.

  PMID 41707654 · PMC12923980 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  DeCAF is a single-sample kTSP classifier using 9 TSP gene pairs that predicts proCAF vs restCAF subtypes from bulk expression data

  pdac cptac external elyada-sc bulk single-sample classifier

• A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

  PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

  Full-text index only

  Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

  tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

  PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

  Full-text index only

  HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

  tcga-luad best brain advanced bulk kaplan-meier pearson

• Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.

  PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  Omics Playground is a user-friendly, interactive self-service platform for in-depth analysis, visualization, and interpretation of transcriptomics and proteomics data, including single-cell RNA-seq.

  l1000 bulk lc-ms single-cell

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample