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).

Publications 1.3k Datasets 392.5k Experiments 1.2k

Assay: gene-expression ✕ Clear

Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

PMID 41904529 · PMC13217986 · Cell communication and signaling : CCS · 2026 · 8 claims · 7 setups

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MITF knockdown and IFNγ stimulation each produce substantial but distinct changes in chromatin accessibility in 624Mel melanoma cells

624mel melanoma atac-seq western motif
Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

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HERV expression differs between primary and metastatic cutaneous melanoma

tcga-skcm metastatic normal selected bulk consensus orf
Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups

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CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC

intestinal colorectal single-cell serum bulk single-cell spatial
Characterizing Response to PARP Inhibitor Treatment Combinations in Advanced Prostate Cancer.

PMID 42193276 · PMC13203762 · Biomedicines · 2026 · 8 claims · 8 setups

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PARPi + ARPi combinations are effective in ARPi-sensitive (C4-2B) and ARPi-resistant (AbiR, MDVR) prostate cancer models, but provide the greatest benefit in ARPi-sensitive cells

c4-2b cck-8 morphology western
Immunosuppressive contribution of tumour-infiltrating B cells in human intrahepatic cholangiocarcinoma and their role in chemoimmunotherapy outcome.

PMID 40889886 · PMC13217081 · Gut · 2026 · 8 claims · 7 setups

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High density of CD20+ B cells in the peritumoural area is associated with improved disease-free survival in iCCA

resected cd45+ scrna-seq peripheral immunohistochemistry kaplan-meier scrna-seq
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

first-trimester decidual spots dnk 10x h&e type
Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

PMID 41159380 · PMC12979040 · Neuro-oncology · 2026 · 8 claims · 8 setups

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A unified UMAP-based transcriptomic landscape built from 888 medulloblastoma and 370 ependymoma tumors reveals distinct clusters corresponding to known and novel molecular subtypes.

medulloblastoma ependymoma healthy shh bulk fusion copy
Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
ChemR23 prevents phenotypic switching of vascular smooth muscle cells into macrophage-like foam cells in atherosclerosis.

PMID 41264461 · PMC13017563 · Cardiovascular research · 2026 · 8 claims · 7 setups

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Non-haematopoietic (vascular) ChemR23 deficiency increases atherosclerotic lesion size and enhances VSMC proliferation and VSMC-derived foam cell formation

apoe adventitia-stripped advanced aortic atherosclerotic bulk single-cell
B-lineage commitment is dependent on a reversible epigenetic switch.

PMID 41266087 · PMC12863259 · Genes & development · 2026 · 8 claims · 8 setups

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B-lymphoid commitment is mediated by a transcription factor-dose-dependent epigenetic switch that suppresses inherent T-lineage potential in early lymphoid progenitors

bone expanded pax5 ebf1 combined atac-seq chip-seq
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
YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

PMID 41431390 · PMC13040214 · Cancer prevention research (Philadelphia, Pa.) · 2026 · 7 claims · 8 setups

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YAP1 nuclear localization and mRNA expression significantly increase in luminal epithelial cells (LEp) with increased age and with genetic risk for breast cancer (e.g., BRCA1/2 mutation carriers)

breast hmec post-stasis 184d-p16sh ihc bulk odds
Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

PMID 41472934 · PMC12745711 · Iranian journal of biotechnology · 2026 · 8 claims · 7 setups

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IL-1β can substitute for PAMPs in inducing DC maturation via a non-canonical pathway distinct from classical TLR-mediated activation

monocyte-derived dendritic bulk principal pathway
Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

stricta long-read short-read hi-c
Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

PMID 41484106 · PMC12881549 · Nature communications · 2026 · 8 claims · 8 setups

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Loss/inhibition of IKKα unexpectedly promotes, rather than suppresses, CRC liver metastasis in patient-derived organoid (PDO) xenograft models.

pdo5 pdo5-derived crc dld1 intrasplenic immunohistochemistry kaplan-meier
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

lung ffpe lymph nonhuman scrna-seq spatial bulk
Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

PMID 41497737 · PMC12765987 · BioMed research international · 2026 · 8 claims · 7 setups

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High RBP7 expression causally increases POP risk

vaginal gwas rbp7 key single-cell mendelian protein-protein
Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

snscc bulk single-nucleus bulk single-nucleus methylation
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine

Experiments

Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

Characterizing Response to PARP Inhibitor Treatment Combinations in Advanced Prostate Cancer.

Immunosuppressive contribution of tumour-infiltrating B cells in human intrahepatic cholangiocarcinoma and their role in chemoimmunotherapy outcome.

Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

ChemR23 prevents phenotypic switching of vascular smooth muscle cells into macrophage-like foam cells in atherosclerosis.

B-lineage commitment is dependent on a reversible epigenetic switch.

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

YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.