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 101

System / cell line: mice ✕ Assay: scrna ✕ Clear

Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

PMID 41826553 · PMC13076647 · EMBO reports · 2026 · 8 claims · 8 setups

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Generated a novel Paneth-cell-specific SIRT1 knockout mouse model (SIRT1 PKO, Sirt1 f/f;Defa6-Cre+)

small immune facs-sorted ileum single-cell facs qpcr
scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

PMID 41769845 · PMC12996892 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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scDock is an integrated pipeline connecting scRNA-seq processing, cell-cell communication inference, and molecular docking-based drug discovery through a single configuration file

diabetic kidney ppia glimepiride-ppia scrna-seq cell-cell type
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 · 7 setups

Has reproduction · 37

Orthogonal engineering with PD1d/IL-2v/IL-33 reprograms adoptively transferred CD8+ T cells into a novel synthetic effector state (C5/TSE) that deviates from canonical TOX+ exhaustion

cd8+ b16-ova ot1 mice scrna-seq flow secretion
CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.

PMID 39645040 · PMC11745947 · Journal of lipid research · 2025 · 8 claims · 8 setups

Has reproduction · 59

Cd14−/− mice exhibit a leaner body shape and are protected from HFD-induced obesity compared to WT mice

epididymal adipose cd14low macrophage bulk scrna-seq pseudotime
PBRM1 Deficiency Reshapes an Immune Suppressive Microenvironment Through Epigenetic Tuning of PBRM1-KDM5C-IL6 Axis in ccRCC.

PMID 41514194 · PMC13042695 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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PBRM1 deficiency increases infiltration of immunosuppressive M2 tumor-associated macrophages (TAMs) and creates an immune-excluded tumor microenvironment

vhl kidney pbrm1 immunodeficient scrna-seq multiplex crispr-cas9
Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

PMID 41723140 · PMC13035813 · Nature communications · 2026 · 8 claims · 8 setups

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Spatial Perturb-Seq simultaneously measures whole transcriptome (cell type), CRISPR barcodes (perturbation), spatial coordinates, and cell-cell interactions through a single Stereo-seq and/or Xenium run.

hippocampus bone brain aav-transduced scrna-seq snrna-seq spatial
Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

PMID 41811178 · PMC12978698 · eLife · 2026 · 8 claims · 8 setups

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Cell type-specific Bayesian and co-expression networks generated from BMSC-OB scRNA-seq data in Diversity Outbred mice can prioritize and contextualize genes underlying human BMD GWAS associations

bmsc-ob genes mesenchymal gtex scrna-seq cellect iterativewgcna
Single-cell dissection of regulated cell death dynamics in ovarian aging.

PMID 41689119 · PMC13005338 · Journal of ovarian research · 2026 · 8 claims · 8 setups

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The RCD landscape of ovarian aging had not previously been characterized at single-cell resolution

ovary serum scrna-seq bulk single-nucleus
Tenascin C(+) myofibroblasts exacerbate vascular neointimal hyperplasia by propagation of nerve-macrophage interactions in mice.

PMID 41617709 · PMC12960667 · Nature communications · 2026 · 7 claims · 8 setups

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A distinct population of Tnc+ myofibroblasts (cluster iFb5) emerges from adventitial fibroblasts during ligation-induced neointimal hyperplasia

carotid adventitial pdgfrα nih-3t3 scrna-seq spatial immunofluorescence
Base barrier cells provide compartmentalization of choroid plexus, brain and CSF.

PMID 41680326 · PMC12971494 · Nature neuroscience · 2026 · 8 claims · 8 setups

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A distinct fibroblast population, ChP base barrier cells (BBCs, formerly type II fibroblasts), exists at the base of the choroid plexus, separate from ChP stromal (type I) fibroblasts

lateral brain mesp1-cre chp scrna-seq multiplex immunofluorescence
Aging-dependent microglial heterogeneity worsens outcomes in models of traumatic brain injury.

PMID 41926211 · PMC13262727 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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Aged TBI brains predominantly harbor proinflammatory NLRP3+ microglia, whereas young TBI brains harbor neuroprotective Lysozyme+ microglia

injured sorted facs-purified cas9-gfp scrna-seq atac-seq untargeted
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 · 8 claims · 6 setups

Has reproduction · 50

IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

cd44+ splenocytes spleen tcr scrna-seq flow spatial
A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat
Loss of SOCS1 in Donor T Cells Exacerbates Intestinal GVHD by Driving a Chemokine-Dependent Pro-Inflammatory Immune Microenvironment.

PMID 41580972 · PMC13042394 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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T cell-specific Socs1 loss intrinsically drives pro-inflammatory T cell differentiation independent of antigen stimulation, with the strongest effects in CD8+ T cells

cd45+ splenic cd8+ sorted single-cell flow bulk
Reciprocal regulation of fibroblast-macrophage equilibrium governs skin integrity.

PMID 41760904 · PMC13043295 · Nature immunology · 2026 · 8 claims · 8 setups

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Dpt+ fibroblasts are required to maintain skin macrophage populations in vivo; their depletion reduces CD64+ and CD11c+ macrophages

facs-sorted skin dpt+ scrna-seq flow cellchat
Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

PMID 41782826 · PMC12955150 · iScience · 2026 · 8 claims · 6 setups

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Tet2-deficient NOD mice transplanted with WT bone marrow show fewer islet-infiltrating lymphocytes beginning 8–10 weeks post-transplant, primarily among CD4+ T cells

islets islet islet-infiltrating cadaveric flow single-cell single-nucleus
Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

PMID 41794902 · PMC13087195 · Scientific reports · 2026 · 8 claims · 5 setups

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Brain CD8+ T cells segregate into two major, mutually exclusive Trm populations: a CXCR6-related immunosuppressive cluster (cd8_c0) present in both aged non-Tg and 5xFAD_WT mice, and an AD-associated stem-like cluster (cd8_c1) present only in 5xFAD mice.

brain-derived brain cd8+ clonally scrna-seq paired cellchat
Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

PMID 41877584 · PMC13103941 · Cancer research communications · 2026 · 8 claims · 6 setups

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Skp2 KO improves survival, drives apoptosis, and induces antitumor immunity in Rb1/Trp53-deficient murine osteosarcoma

tumors same osteosarcoma skp2 scrna-seq mutation copy-number
ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

PMID 41896465 · PMC13043298 · Nature immunology · 2026 · 8 claims · 8 setups

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ZFP148 is enriched in CD8+ T progenitor (T PRO) cells and its expression declines during differentiation into effector (T EFF) and exhausted (T EX) cells

p14 splenic cd8+ b16-gp scrna-seq flow tcr
Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.

PMID 41675929 · PMC12886473 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 2 setups

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Both innate and adaptive immune responses were activated in M. fortis peripheral blood at 10 dpi, while activation was not obvious in Kunming mice at the same time point

pbmcs single-cell qpcr

Experiments

Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.

PBRM1 Deficiency Reshapes an Immune Suppressive Microenvironment Through Epigenetic Tuning of PBRM1-KDM5C-IL6 Axis in ccRCC.

Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

Single-cell dissection of regulated cell death dynamics in ovarian aging.

Tenascin C(+) myofibroblasts exacerbate vascular neointimal hyperplasia by propagation of nerve-macrophage interactions in mice.

Base barrier cells provide compartmentalization of choroid plexus, brain and CSF.

Aging-dependent microglial heterogeneity worsens outcomes in models of traumatic brain injury.

Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

Loss of SOCS1 in Donor T Cells Exacerbates Intestinal GVHD by Driving a Chemokine-Dependent Pro-Inflammatory Immune Microenvironment.

Reciprocal regulation of fibroblast-macrophage equilibrium governs skin integrity.

Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.