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).

• SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven two-cell totipotency transcriptional program in the mouse embryo.

  PMID 41697236 · PMC12908936 · eLife · 2026 · 8 claims · 5 setups

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  Maternal SETDB1 is required for mouse preimplantation development beyond the eight-cell stage

  2-cell single-embryo degs embryo single-embryo principal

• Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.

  PMID 41699318 · PMC13061605 · Nature neuroscience · 2026 · 8 claims · 8 setups

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  Rgl1 is the progenitor of the mesDA neuronal lineage

  embryonic developing wa09 bulk scrna-seq ligand-receptor

• A cell atlas of multiple liver organoids and the fetal liver based on scRNA-seq.

  PMID 41736863 · PMC12927097 · iScience · 2026 · 8 claims · 8 setups

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  A unified liver organoid cell atlas of 217,025 high-quality cells was constructed by integrating scRNA-seq data from 15 organoid samples across 9 studies with human fetal liver data (5-19 weeks gestation)

  liver fetal endoderm-derived mesoderm-derived scrna-seq pseudotime pearson

• Transcriptome-based high-frequency recurrence index predicts frequent recurrence in non-muscle-invasive bladder cancer after Bacillus Calmette-Guérin therapy.

  PMID 41749284 · PMC13040970 · BMC medicine · 2026 · 8 claims · 7 setups

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  A 75-gene HfRI signature predicts high-frequency recurrence (≥2 recurrences) in NMIBC patients

  nmibc uromol2021 bulk microarray rna-seq

• MafB is a conserved transcriptional regulator of macrophage development and functional identity across tissues and species.

  PMID 41759510 · PMC7618887 · Immunity · 2026 · 8 claims · 8 setups

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  MafB is required for full differentiation of bone-marrow-derived macrophages (BMDMs) in vitro and for development of most RTMs in vivo

  bmdms peritoneal rtms irradiated bulk hashtag-barcoded intracellular

• 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

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• Gene expression profiling identifies potential biomarkers for vaso-occlusive episodes in sickle cell disease.

  PMID 41797711 · PMC13041688 · JCI insight · 2026 · 8 claims · 5 setups

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  Pathways linked to complement activation, coagulation, and IL-6/JAK/STAT3 signaling are enriched during VOEs in CD45+ leukocytes

  cd45+ cd71+ plasma bulk gsva plasma

• MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

  PMID 41800385 · PMC12961272 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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  MIRit is a comprehensive, open-source R/Bioconductor framework for integrative miRNA–mRNA analysis that supports both paired and unpaired datasets using statistically appropriate methods.

  myocardial ccrcc brodmann synthetic mirna-seq microarray small

• Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment.

  PMID 41817317 · PMC13223553 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 8 claims · 7 setups

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  High-grade histopathologic TIL infiltration is associated with significantly prolonged overall survival in breast and lung cancer BM.

  breast lung histopathologic sequencing tcr

• Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats.

  PMID 41862462 · PMC13168590 · Nature communications · 2026 · 8 claims · 7 setups

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  Gene regulatory responses to endurance exercise training (EET) are predominantly tissue-specific rather than shared across tissues

  tissues same skm-gn rna-seq atac-seq rrbs

• Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes.

  PMID 41898740 · PMC13026113 · International journal of molecular sciences · 2026 · 7 claims · 7 setups

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  Pigmented potato cultivars (DG26, DJ247) accumulate higher levels of flavonoids and linoleic acid derivatives than the white-fleshed cultivar (AG594)

  potato bioinformatic untargeted rna-seq rt-qpcr

• Transcriptomic insights into thermal manipulation and heat stress in skeletal muscles of broiler chickens.

  PMID 41905070 · PMC13054079 · Poultry science · 2026 · 6 claims · 5 setups

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  Acute HS induces pronounced transcriptional changes including activation of immune signaling and stress-responsive pathways and suppression of metabolic/energy-related processes

  pectoralis broiler muscle bulk qrt-pcr body

• Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice.

  PMID 41922840 · PMC13171603 · Nature microbiology · 2026 · 8 claims · 7 setups

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  Inflammatory macrophages accumulate in joint-associated tissue during the chronic stage of CHIKV infection and show an activated, pro-inflammatory, MHC-II+ transcriptional programme

  ankle ipsilateral computational pfa-fixed rt-qpcr single-cell gene

• ASTROREPOMICS: A curated transcriptomic database for reproductive biology in space.

  PMID 41940322 · PMC13049440 · iScience · 2026 · 8 claims · 6 setups

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  ASTROREPOMICS integrates 17 rigorously normalized and batch-corrected transcriptomic datasets spanning multiple species and reproductive tissues

  pooled mus rattus pca-based combat differential

• Peripheral Immune and Metabolic Dysregulation in Migraine, Ménière's Disease, and Vestibular Migraine: A Single-Cell Atlas Study.

  PMID 41953397 · PMC13054517 · Human mutation · 2026 · 8 claims · 8 setups

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  T cell abundance is significantly increased in MI compared to HC, while monocyte abundance is reduced, identifying T cells as a key pathogenic cell type

  pbmcs pbmc-derived degs pbmc single-cell differential kegg

• Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

  PMID 41975179 · PMC13250061 · Nature communications · 2026 · 8 claims · 8 setups

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  Epithelial cells in mLNs and matched mLN+ primary tumors (mLN+PTs) show enhanced cancer stemness (higher CytoTRACE scores) compared to mLN-negative and normal samples.

  patient-matched mln epithelial tcga-luad scrna-seq spatial cytotrace

• Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrants.

  PMID 42023153 · PMC13098507 · iScience · 2026 · 8 claims · 5 setups

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  Neonatal and adult CD8+ RTEs are phenotypically and functionally distinct despite equivalent post-thymic maturation time

  splenic neonatal sorted flow single-cell differential

• Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms.

  PMID 42028238 · PMC13100350 · Computational and structural biotechnology journal · 2026 · 8 claims · 5 setups

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  A Regulation Ratio (RR), calculated as the ratio of gene-length-normalized POP-seq peak density to ATAC-seq peak density, quantifies the relative balance of post-transcriptional versus transcriptional regulation for individual genes

  hek293 computational atac-seq pop-seq rna-seq

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk