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).
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Has reproduction · 67
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.
PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups
RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical
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Has reproduction · 94
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.
PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups
Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal
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Has reproduction
Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.
PMID 41001759 · PMC12713092 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 6 claims · 8 setups
Human primary GBMs contain both tumor-originated pericytes (T-PCs) and normal-originated pericytes (N-PCs) with distinctive cell-intrinsic features.
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Has reproduction · 59
Single-Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression.
PMID 34825784 · PMC8787427 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022 · 8 claims · 6 setups
Human NP contains six transcriptionally distinct NPC subpopulations: HT-CLNPs, effector NPCs, homeostatic NPCs, regulatory NPCs, fibroNPCs, and adhesion NPCs
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Has reproduction · 90
A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.
PMID 34140473 · PMC8211662 · Nature communications · 2021 · 8 claims · 5 setups
The human post-implantation epiblast transitions from a naïve to a primed pluripotent state, with naïve markers (KLF4, KLF17, PRDM14, etc.) downregulated and primed markers (FGF2, DNMT3B, SOX11, etc.) upregulated between pre- and post-implantation stages
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Has reproduction · 50
Microglial Fkbp5 Impairs Post-Stroke Vascular Integrity and Regeneration by Promoting Yap1-Mediated Glycolysis and Oxidative Phosphorylation.
PMID 41355597 · PMC13042415 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups
A post-stroke perivascular microglial niche (stroke-VAM) exists, characterized by low M2 marker expression and elevated glycolysis, OXPHOS, and phagocytic activity.
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Has reproduction · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA
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Has reproduction
Mapping the Development of Human Spermatogenesis Using Transcriptomics-Based Data: A Scoping Review.
PMID 39000031 · PMC11241379 · International journal of molecular sciences · 2024 · 8 claims · 8 setups
scRNA-seq of human testis reveals major transcriptional modifications occurring around 11 years of age, marking a transition toward the adult cellular state
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Has reproduction · 50
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.
PMID 36450262 · PMC9792173 · Cell reports · 2022 · 7 claims · 7 setups
Following transient CD4 depletion, IL-21-producing Tfh cells do repopulate but are outnumbered by immunomodulatory CD4 T cells (Tregs, Th17), and IL-21+ frequency remains low within activated CD4 T cells.
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Has reproduction · 70
Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.
PMID 33723257 · PMC7961017 · Nature communications · 2021 · 7 claims · 7 setups
Proportions of activated and proliferating CD8+ T cells (cluster C16/activated EM) are significantly higher in responders before and during therapy
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Has reproduction · 88
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.
PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups
CD39+CD8+ TILs are a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells within ccRCC tumors
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Has reproduction · 37
Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.
PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 6 setups
Orthogonal engineering of CD8+ T cells to co-secrete IL-2v and IL-33 (with PD-1 decoy) drives a novel synthetic effector state (C5 T_SE) that deviates from canonical PD-1+TOX+ exhaustion.
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Has reproduction · 59
Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.
PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups
Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes