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).

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

  PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

  hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry

• Niacin promotes motor function recovery after spinal cord injury via Hcar2-dependent microglia immunometabolic regulation.

  PMID 42068080 · PMC13135113 · Clinical and translational medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Hcar2 is a microglia-enriched gene whose spinal cord expression is upregulated after SCI, peaking at 7 days post-injury

  spinal c57bl bv2 single-cell bulk sci

• MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration.

  PMID 41634555 · PMC12955011 · BMC bioinformatics · 2026 · 8 claims · 5 setups

  Full-text index only

  MUUMI unifies statistical meta-analysis and network-based omics data integration within a single analytical R package framework

  lung integrated ranked thp-1 sequencing microarray statistical

• scDecorr: feature decorrelation based representation learning enables self-supervised alignment of multiple single-cell experiments.

  PMID 42056283 · PMC13128840 · Scientific reports · 2026 · 7 claims · 1 setups

  Full-text index only

  scDecorr learns robust cell representations of unlabelled single-cell experiments in a negative-sample-free self-supervised fashion using feature decorrelation

  datasets scrna-seq

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

  PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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  H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

  tumor hnacc epithelial accb single-cell scrna-seq copy

• Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.

  PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 68

  RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)

  endometrial in-house bulk rif-degs meta-analysis sequencing immune

• Developmental convergence and divergence in human stem cell models of autism.

  PMID 41611887 · PMC12999519 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  Different ASD-associated mutations show the largest mutation-specific transcriptional changes early in hCO differentiation but converge on shared transcriptional changes as development progresses

  cortical hips induced hco bulk whole-genome ip-ms

• Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

  PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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  13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

  13-lined retina 13lgs retinal single-cell scrna-seq chromvar

• 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

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

  PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

  patients bulk colorectal epithelial clinical bulk single-cell

• Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

  PMID 41837870 · PMC13248853 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 6 setups

  Full-text index only

  Micropatterned cardioids generated from hiPSCs co-develop mesoderm-heart and endoderm-foregut/liver lineages, including a previously unreported non-neural ectoderm population.

  hipsc-derived crispr-engineered micropatterned scrna-seq whole-mount clearing single-cell

• Pre-existing cell states predict resistance to multiple treatments.

  PMID 41916275 · PMC13261651 · Cell genomics · 2026 · 8 claims · 5 setups

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  Rare melanoma clones can develop resistance to multiple diverse treatments simultaneously, not just single treatments

  wm989 time-lapse barcode single-cell

• Spatial multi-omics unveils the monoclonal origin, neuroendocrine plasticity, and microenvironment niches in combined small-cell lung cancer.

  PMID 41966692 · PMC13130634 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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  Different histologic components within cSCLC tumors share a monoclonal origin

  ffpe sections tumor luad multi-region spatial single-nucleus

• Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair.

  PMID 41617708 · PMC12960685 · Nature communications · 2026 · 8 claims · 8 setups

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  A genetically engineered mouse model (Krt14-CreER; LSL-rtTA-EGFP; TetO-OSKM-mCherry, 'Epi-iOSKM') enables transient, reversible, mosaic OSKM expression in interfollicular epidermal cells without inducing pluripotency or teratoma risk

  epidermis sorted epidermal ife immunostaining single-cell pseudotime

• An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.

  PMID 41792167 · PMC13087180 · Scientific data · 2026 · 8 claims · 8 setups

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  An improved chromosome-level genome assembly of C. savignyi was generated using Illumina short reads, ONT long reads, and Hi-C data.

  savignyi illumina oxford hi-c