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).

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

  PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

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  scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

  onek1k-derived onek1k-based immune brain simulated two-sample stage

• Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

  PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts

  tcga paired thbs2+ scrna-seq wgcna scrna-seq gsea

• 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

• 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

• A Novel Human Cellular System for Studying Normal Aging and for Anti-Aging Discovery.

  PMID 41556081 · PMC12816977 · Aging cell · 2026 · 6 claims · 8 setups

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  In vitro hTSC-derived STBs recapitulate in vivo CTB-STB maturation and major cellular aging features, including multinucleation, hormone secretion, cell cycle arrest, genome instability, epigenetic changes, transposable element activation, and SASPs.

  peri-implantation first-trimester term-stage musc scrna-seq bulk linear

• Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression.

  PMID 41559111 · PMC12873405 · NPJ systems biology and applications · 2026 · 7 claims · 8 setups

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  NR2F1 is a central transcription factor in LUAD progression, identified independently through GRN architecture transitions and gene regulation dynamics analysis

  luad epithelial myeloid nr2f1 single-cell gene binding

• Single-Cell Transcriptomic Atlases of Camels and Cattle Unravel Molecular Evolution of Digestive and Metabolic Systems.

  PMID 41632085 · PMC13067795 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

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  Generated single-cell/nucleus transcriptomic atlases of camels and cattle across 54 tissues, identifying 124 cell types (78 in camels, 106 in cattle, 59 shared)

  camel bovine structural orthologous scrna-seq spatial scenic

• Integrative single-cell analysis uncovers distinct tumour microenvironment ecotypes and immune evasion across skin cancers.

  PMID 41636115 · PMC12869349 · Clinical and translational medicine · 2026 · 7 claims · 8 setups

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  A malignant NARS2+NDUFC2+ melanoma cell subpopulation with reduced MHC-I expression is enriched in advanced-stage tumours and associated with worse survival and immunotherapy response.

  skin prognosis melanoma macrophage single-cell bulk immunofluorescence

• Aurkb deficiency disrupts microglial development, homeostasis and hinders remyelination following cuprizone-induced demyelination.

  PMID 41704758 · PMC12907124 · iScience · 2026 · 8 claims · 8 setups

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  Aurkb is upregulated in a subset of fetal/neonatal microglia and in microglia following CPZ-induced demyelination and in MS patient microglia

  microglia brain neonatal corpus scrna-seq western immunofluorescence

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

  PMID 41364805 · PMC13012255 · Blood cancer discovery · 2026 · 7 claims · 8 setups

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  IFN-γ signaling after autologous stem cell transplant (ASCT) is associated with markers of impaired CD8+ T-cell memory phenotype

  cd138neg cd138pos bone cd8+ single-cell bulk whole-genome

• Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX.

  PMID 41723123 · PMC13035843 · Nature communications · 2026 · 8 claims · 6 setups

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  CAMEX outperforms state-of-the-art integration methods on cross-species scRNA-seq benchmarking datasets ranging from one to eleven species

  liver ovary pancreas testis scrna-seq type

• A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

  PMID 41514053 · PMC12858409 · Nature cancer · 2026 · 8 claims · 6 setups

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  Generated a single-cell Immune Atlas of 1,397,272 BM cells from 337 NDMM participants (263 discovery, 74 validation) using scRNA-seq

  cd138 bone ndmm single-cell cytogenetic disease

• Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.

  PMID 41622528 · PMC12916010 · Molecular biology and evolution · 2026 · 7 claims · 8 setups

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  Cattle and yak testes contain seven types of spermatogonia, ten spermatocyte subtypes, and ten spermatid types with largely conserved transcriptional programs governing spermatogenic fate transitions.

  testicular spermatocytes spermatids bc1 single-cell chromosome hematoxylin

• Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

  PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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  cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

  discoideum single-cell scrna-seq dissecting

• miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.

  PMID 41811946 · PMC12978216 · Science advances · 2026 · 8 claims · 8 setups

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  miR-203 is required for a timely totipotency-to-pluripotency transition during early mouse embryogenesis

  preimplantation 8-cell mice mir-203 qrt-pcr genotyping time-lapse

• Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

  PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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  DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

  ipsc embryonic ipsc-derived bulk scrna-seq qpcr

• Rtf1-dependent transcriptional pausing regulates cardiogenesis.

  PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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  Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

  zebrafish embryo embryonic mescs crispr situ shrna

• 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