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).

• A pan-cancer single-cell transcriptomic atlas of human bone metastases.

  PMID 41619722 · PMC12923970 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Constructed a pan-cancer single-cell transcriptomic atlas of 62 human bone metastases (predominantly spinal) across 13 primary cancer types, with paired primary tumor and normal bone marrow samples.

  bone paired plasmacytoma malignant scrna-seq ihc infercnv

• 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

• ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.

  PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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  ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.

  pc9 paired-end sorted atac-seq quality read

• 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

• Innate antiviral and immune functions associated with the HIV reservoir decay after anti-PD-1 therapy.

  PMID 41680482 · PMC12920136 · Nature medicine · 2026 · 7 claims · 7 setups

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  Anti-PD-1 therapy triggers a rapid (within 24 hours) systemic cascade of increased IFN/antiviral, monocyte, and CD8+ T cell effector transcriptomic modules alongside decreased plasma TGFβ.

  pbmcs plasma pbmc publicly bulk plasma integrated

• SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

  PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

  tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based

• Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

  PMID 41723121 · PMC12932787 · Nature communications · 2026 · 8 claims · 8 setups

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  Different tumor cell transcriptomic states organize into distinct spatial clusters, or 'villages', each supported by a unique surrounding microenvironment

  liver malignant non-malignant tumor single-cell immunofluorescence non-negative

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• A disease model resource reveals core principles of tissue-specific cancer evolution.

  PMID 41741657 · PMC13149333 · Nature · 2026 · 8 claims · 8 setups

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  The Mouse Cancer Cell line Atlas (MCCA) is a broad-utility resource of 590 comprehensively characterized mouse cancer cell line models spanning 22 lineages and 46 disease types, accessible via a web portal (www.mcca.tum.de)

  mcca tumour immunocompetent paca whole-genome microscopy-based histopathology

• Targeting the Golgi apparatus enhances PD-L1 blockade and synergizes with oxaliplatin to improve immunotherapy efficacy.

  PMID 41791704 · PMC13053745 · The Journal of biological chemistry · 2026 · 8 claims · 8 setups

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  PCR-Lip (chondroitin sulfate/retinoic acid liposome) disrupts Golgi ribbon structure into fragmented ministacks and reduces Golgi enzyme (Man II, GalT) activity

  4t1 exosomes transmission immunofluorescence enzymatic

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.

  PMID 41805684 · PMC12975130 · eLife · 2026 · 8 claims · 8 setups

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  EPB41L4A-AS1 acts in cis to enhance transcription of the proximal EPB41L4A gene

  mcf-7 epb41l4a-as1 rna-seq rt-qpcr single-molecule

• AGPAT3 reshapes tumor cell vulnerability to IFNγ-mediated ferroptosis and enhances immunotherapy efficacy through lipid remodeling.

  PMID 41807033 · PMC12983827 · Journal for immunotherapy of cancer · 2026 · 8 claims · 8 setups

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  A ferroptosis-driver gene signature (FD.sig) and machine learning model (FD.model) can predict ICI response

  pan-cancer tcga a375 machine single-cell bulk

• SMARCA4/2 loss reduces BCL-xL expression and confers a druggable MCL1 dependency in cancer.

  PMID 41807550 · PMC13249849 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  MCL1 inhibition is synthetic lethal with SMARCA4/2 loss in SCCOHT and NSCLC cells

  nsclc lung smarca4 bin-67 genome-wide drug colony

• Mapping Genetic Regulation of Transcription to Identify Functional Variants and Genes Associated with Pancreatic Cancer Risk.

  PMID 41824785 · PMC13205582 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A genome-wide cis-eQTL meta-analysis of 482 pancreatic tissues (177 TCGA tumor + 305 GTEx normal) identified 1,123,483 significant SNP-gene pairs, 709,720 unique eQTLs, and 13,758 eGenes (FDR<0.05)

  tcga chinese significant egenes cis-eqtl gwas variant

• Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

  PMID 41840060 · PMC13125306 · Scientific reports · 2026 · 8 claims · 7 setups

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  IDC exhibits significantly higher CNV burden than DCIS, supporting progressive genomic instability during tumor evolution

  her2-positive epithelial malignant tcga-brca single-cell spatial infercnv

• Single-cell transcriptome analysis reveals DNMT1(+) epithelial cells promote lymphatic metastasis via CXCL17-mediated TAM infiltration.

  PMID 41845371 · PMC13107741 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  DNMT1+ epithelial cells, characterized by high epithelial-mesenchymal transition potential, show a propensity for lymph node metastasis in bladder cancer

  bladder scrna-seq um-uc-3 genomic single-cell cell-cell western

• Multi-omics evaluation of cell lines as models for metastatic prostate cancer.

  PMID 41876625 · PMC13171877 · Communications biology · 2026 · 8 claims · 8 setups

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  Substantial genomic differences exist between metastatic prostate cancer patient samples and prostate cancer cell lines, including hotspot mutations largely absent from cell lines.

  prostate metastatic su2c tcga somatic copy bulk

• Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

  PMID 41882353 · PMC13216075 · Nature · 2026 · 8 claims · 8 setups

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  GluN1 and GluN2B NMDAR subunits are ectopically expressed in cancer cells of human TNBC tumours

  breast tnbc 4t1-nmdar orthotopic bulk spatial immunofluorescence

• A Single-Cell Atlas of Pan-Cancer Liver Metastasis Reveals Dynamic Cellular Programs Driving Metastatic Progression and Immune Modulation.

  PMID 41884334 · PMC13010057 · Research (Washington, D.C.) · 2026 · 8 claims · 4 setups

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  A pan-cancer single-cell transcriptomic atlas of liver metastasis was constructed from 100 scRNA-seq samples (75 individuals, 16 studies), profiling 460,337 cells into 121 distinct cellular subtypes.

  epithelial liver-related scrna-seq copy cellular