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).

• 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

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

  PMID 41643060 · PMC13073339 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

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  Testicular endothelial cells (TECs) function as a central signaling hub coordinating intercellular communication within the human testicular interstitium

  testicular testis leydig diabetic single-cell integrative cell-cell

• 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

• Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

  PMID 41593306 · PMC12868835 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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  Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

  pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian

• transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

  PMID 41645434 · PMC12930851 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  transFusion is a comprehensive, web-based platform for integrated analysis of scRNA-seq and 10x Visium spatial transcriptomics data requiring no parameter configuration

  breast scrna-seq 10x cellphonedb

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

  PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

  bmmc pbmc foetal cis-regulatory enhancer-promoter scalability

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups

  Has reproduction · 71

  109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules

  pbmc shared hub pbmcs weighted kegg differential

• Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

  PMID 41880523 · PMC13154832 · GigaScience · 2026 · 7 claims · 8 setups

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  Hallmarks of malignancy and cell cycle regulatory pathways are consistently enriched across single-cell, bulk, and spatial transcriptomic modalities, promoting tumor cell proliferation and progression.

  tumor gbm normal wild-type single-cell bulk microarray

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna

• Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders.

  PMID 41653922 · PMC13034722 · Molecular cell · 2026 · 8 claims · 8 setups

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  Heterozygous de novo missense mutations in RING1 and RNF2 are found in individuals with neurodevelopmental/intellectual disability phenotypes

  cohorts prc1 ring1a elegans variant structural western

• Single-cell and isoform-specific translational profiling of the mouse brain.

  PMID 41708856 · PMC13102718 · Nature · 2026 · 8 claims · 8 setups

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  Ribo-STAMP coupled with short-read and long-read single-cell RNA-seq enables isoform-sensitive single-cell translatome profiling in the brain

  cortical curated hippocampus bulk immunocytochemistry eclip

• STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing sarcoma aggressiveness.

  PMID 41950086 · PMC13079922 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  STAG2 loss does not globally attenuate EWS-FLI1 activity but reprograms its chromatin binding, redirecting it from short (1-4x) GGAA-repeat sites toward long/multimeric (≥5x) GGAA-repeat microsatellite enhancers

  a673 tc-71 chip-seq immunoblot atac-seq