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).

• 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

• 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 Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• 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

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• TOPK Suppresses the CD8(+) T Cell Antitumor Immunity via Modulation of IRF5 Expression.

  PMID 41868885 · PMC13003159 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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  A TOPK+ subset of tumor-infiltrating CD8+ T cells exists in melanoma at higher frequency than in normal lymph nodes and shows suppressed cytotoxic/cytokine programs.

  tumor-infiltrating melanoma b16-f10 unspecified scrna-seq flow multiplex

• Tree shrew immune cell atlas identifies NR1H3⁺ tissue macrophages with conserved anti-inflammatory function.

  PMID 41957356 · PMC13223331 · Nature communications · 2026 · 8 claims · 8 setups

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  A single-cell/single-nucleus RNA-seq atlas across 12 tree shrew tissues identifies 39 distinct immune and non-immune cell types, providing a reference resource for tree shrew immunology

  tree single-cell scrna-seq cross-species functional

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.

  PMID 41128661 · PMC12877754 · Cancer discovery · 2026 · 8 claims · 8 setups

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  RMC-9945 exerts durable antitumor activity in early-stage liver metastasis but has diminished therapeutic effect in advanced metastatic disease

  aktp colorectal drug single-cell rnascope

• Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

  PMID 41779856 · PMC12959402 · Science advances · 2026 · 7 claims · 6 setups

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  Lung tumors drive expansion of both CD27+ and CD27- pulmonary γδ T cells, which acquire distinct spatial and phenotypic changes in the tumor microenvironment

  spc-cre+ microdissected sorted merged flow confocal single-cell

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

  PMID 41632074 · PMC12954174 · GigaScience · 2026 · 8 claims · 5 setups

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  Generated a multi-organ snATAC-seq atlas of 9 adult rat organs comprising 25 libraries and over 110,000 cells

  organs publicly snatac-seq group-level snatac-seq scrna-seq gene

• MafB is a conserved transcriptional regulator of macrophage development and functional identity across tissues and species.

  PMID 41759510 · PMC7618887 · Immunity · 2026 · 8 claims · 8 setups

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  MafB is required for full differentiation of bone-marrow-derived macrophages (BMDMs) in vitro and for development of most RTMs in vivo

  bmdms peritoneal rtms irradiated bulk hashtag-barcoded intracellular

• AICellType: a large language model-based platform for accurate cell type annotation.

  PMID 42001469 · PMC13092268 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  Claude 3.5 Sonnet achieved the best overall performance among 79 benchmarked LLMs for cell type annotation, balancing accuracy, robustness, speed, and cost-efficiency

  single-cell immune pbmc in-house llm-based scrna-seq spatial

• Limited protection against early-life lung murine cytomegalovirus infection results from deficiency of cytotoxic CD8 T cells.

  PMID 42008567 · PMC13128127 · PLoS pathogens · 2026 · 9 claims · 9 setups

  Full-text index only

  Expansion of endogenous MCMV-specific CD8 T cells is delayed in early life due to a low precursor frequency of peripheral αβ T cells

  peripheral spleen polyclonal neonatal pmhc-i mhc-ii flow

• CD38 expression by neonatal human naive CD4+ T cells shapes their distinct metabolic and tolerogenic properties.

  PMID 41746743 · PMC13078883 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  CD38 is markedly more highly expressed on cord blood (CB) naive CD4+ T cells than adult blood (AB) naive CD4+ T cells, with an age-dependent gradient from fetal to pediatric life.

  pbmcs sorted scrna-seq naive flow bulk compass

• Dietary conjugated linoleic acid enhances resistance to Salmonella infection by promoting PPARγ-mediated metabolic reprogramming and effector function in CD8⁺ T cells.

  PMID 41964110 · PMC13078244 · Gut microbes · 2026 · 8 claims · 12 setups

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  Dietary CLA supplementation enhances host resistance to Salmonella Typhimurium infection

  ileal mice serum culture 16s untargeted bulk

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral