{
  "version": "2026-08-17",
  "curated_note": "Published-paper evidence only. These four studies do not have a locally processed single-cell matrix on LACA. Numbers are transcribed from the open PMC full text and supplements; they are not re-derived from raw reads.",
  "studies": {
    "three-cohort-centenarian-2025": {
      "dataset_id": "three-cohort-centenarian-2025",
      "label": "Three-Cohort Centenarian Atlas (NK rejuvenation)",
      "journal": "eBioMedicine",
      "year": "2025",
      "pmid": "40945050",
      "pmcid": "PMC12571583",
      "doi": "10.1016/j.ebiom.2025.105922",
      "license": "CC BY-NC-ND 4.0",
      "license_note": "Non-derivative licence. LACA shows captions and links to the publisher/PMC originals. Do not recolour or rehost these UMAPs as LACA figures.",
      "access": {
        "status": "controlled",
        "status_label": "Controlled access",
        "raw_summary": "Lingao scRNA is GSA-Human HRA011570 (controlled). Rugao HRA002867 is also controlled. Japan RIKEN SC2018 and age-control GSE158055 are public reuse, not a local centenarian matrix.",
        "local_matrix": false,
        "accessions": [
          {"id": "HRA011570", "kind": "GSA-Human", "role": "Lingao discovery (controlled)", "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA011570"},
          {"id": "HRA002867", "kind": "GSA-Human", "role": "Rugao reuse (controlled)", "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA002867"},
          {"id": "RIKEN SC2018", "kind": "project page", "role": "Japan cohort", "url": "http://gerg.gsc.riken.jp/SC2018/"},
          {"id": "GSE158055", "kind": "GEO", "role": "Age-control reuse", "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158055"}
        ]
      },
      "links": {
        "pubmed": "https://pubmed.ncbi.nlm.nih.gov/40945050/",
        "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/",
        "article": "https://www.sciencedirect.com/science/article/pii/S2352396425003664"
      },
      "sample_splits": [
        {"site": "Lingao (Hainan)", "cen": 17, "off": 9, "ctl": 14, "note": "Discovery scRNA / TCR"},
        {"site": "Rugao (Jiangsu)", "cen": 7, "off": 6, "ctl": 9, "note": "Reuse of HRA002867"},
        {"site": "Japan (RIKEN)", "cen": 7, "off": 2, "ctl": 3, "note": "Public SC2018"},
        {"site": "Paper headline total", "cen": 31, "off": 17, "ctl": 26, "note": "Includes CyTOF / flow subsets; not a single matrix"}
      ],
      "assay_subsets": [
        {"assay": "scRNA-seq reported total", "cen": 19, "off": 10, "ctl": 15},
        {"assay": "CyTOF (Lingao)", "cen": 9, "off": 6, "ctl": 5},
        {"assay": "Flow (Lingao)", "cen": 10, "off": 7, "ctl": 7}
      ],
      "figures": [
        {"id": "Fig.1", "title": "Global PBMC immune landscape", "caption": "UMAP of 10 major clusters with group proportions and box plots across CEN / offspring / control.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig1/"},
        {"id": "Fig.2", "title": "CyTOF immune landscape", "caption": "11 CyTOF clusters, t-SNE and percentage box plots validating the scRNA shifts.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig2/"},
        {"id": "Fig.3", "title": "CD4+ T phenotypes", "caption": "Nine CD4 subsets, trajectories, TF networks and RUNX3 flow validation.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig3/"},
        {"id": "Fig.4", "title": "CD8+ T phenotypes", "caption": "Six CD8 subsets, cytotoxic / MHC programmes and delayed naive-to-CTL polarisation.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig4/"},
        {"id": "Fig.5", "title": "NK and γδ T phenotypes", "caption": "Seven NK / γδ subsets with RUNX3 / KLF4 and flow confirmation.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig5/"},
        {"id": "Fig.6", "title": "Centenarian NK signatures", "caption": "Cytotoxic genes, granzyme B / perforin after stimulation, and rejuvenated membrane receptors.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig6/"},
        {"id": "Fig.7", "title": "NK–T cell–cell communication", "caption": "CellChat heatmaps: enhanced MHC-I, CD99 and MIF between NCAM1-low NK and T cells.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12571583/figure/fig7/"}
      ],
      "core_tables": [
        {
          "id": "composition-shifts",
          "title": "CEN vs control composition shifts (paper-reported)",
          "source": "Main text; Kruskal–Wallis + Dunn. Exact percentages live in the figure box plots, not a numeric table.",
          "columns": ["Compartment", "Direction in CEN vs CT", "Reported P"],
          "rows": [
            ["B cells", "Decreased", "P<0.05"],
            ["CD4+ T", "Decreased", "P<0.001"],
            ["NK cells", "Increased", "P<0.01"],
            ["MAIT", "Decreased", "P<0.01"],
            ["Proliferative T / NK", "Increased", "P<0.01"],
            ["CD4+ CTL", "Increased", "paper-reported"],
            ["CD27+ Tcm / Th17 / Tn", "Decreased", "paper-reported"],
            ["CD8+ CTL / CMC1+", "Increased", "paper-reported"],
            ["RUNX3 in CD56dim NK", "Increased", "P<0.001"],
            ["RUNX3 in CD4+ T", "Increased", "P<0.05"]
          ]
        },
        {
          "id": "cohort-split",
          "title": "Where the 31 / 17 / 26 headline counts come from",
          "source": "Methods / results sample accounting in PMC12571583.",
          "columns": ["Site", "CEN", "Offspring", "Control", "Note"],
          "rows": [
            ["Lingao", "17", "9", "14", "Discovery"],
            ["Rugao", "7", "6", "9", "HRA002867"],
            ["Japan", "7", "2", "3", "RIKEN SC2018"],
            ["Headline total", "31", "17", "26", "Not one open matrix"]
          ]
        }
      ],
      "supplements": [
        "mmc1.docx — supplementary figures",
        "Table S1 — CyTOF 42-antibody panel",
        "Table S2 — flow-cytometry antibodies",
        "Table S3 — Lingao / Rugao clinical information",
        "Table S4 — per-subject scRNA QC",
        "Table S5 — marker / DEG lists"
      ]
    },
    "rugao-blue-zone-2022": {
      "dataset_id": "rugao-blue-zone-2022",
      "label": "Rugao 'Blue Zone' Longevity Immune Remodeling",
      "journal": "Advanced Science",
      "year": "2022",
      "pmid": "36354175",
      "pmcid": "PMC9799020",
      "doi": "10.1002/advs.202204849",
      "license": "CC BY 4.0",
      "license_note": "Open licence. Captions and published numbers may be shown with attribution. Raw reads remain GSA-Human controlled.",
      "access": {
        "status": "controlled",
        "status_label": "Controlled access",
        "raw_summary": "Raw sequence data are in NGDC BioProject PRJCA011218 / GSA-Human HRA002867 (controlled). No local h5ad on LACA.",
        "local_matrix": false,
        "accessions": [
          {"id": "PRJCA011218", "kind": "NGDC BioProject", "role": "Study project", "url": "https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA011218"},
          {"id": "HRA002867", "kind": "GSA-Human", "role": "Raw scRNA / TCR (controlled)", "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA002867"}
        ]
      },
      "links": {
        "pubmed": "https://pubmed.ncbi.nlm.nih.gov/36354175/",
        "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/",
        "article": "https://onlinelibrary.wiley.com/doi/10.1002/advs.202204849"
      },
      "sample_splits": [
        {"site": "Rugao scRNA-seq", "cen": 7, "off": 6, "ctl": 9, "note": "Ages CEN 100–108; offspring 61–83; control 60–77"},
        {"site": "Flow validation", "cen": 30, "off": 30, "ctl": 30, "note": "Independent FACS, not the scRNA donors"}
      ],
      "figures": [
        {"id": "Fig.1", "title": "PBMC single-cell profile", "caption": "Study design, t-SNE of major lineages, per-participant cell counts and T-cell subclustering.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0001/"},
        {"id": "Fig.2", "title": "CPC enriched, NPC depleted", "caption": "Log-odds enrichment plus scRNA and FACS box plots of cytotoxic vs naive-like T cells.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0002/"},
        {"id": "Fig.3", "title": "Longevity vs aging T-cell maps", "caption": "Comparison against Zheng et al. and Mogilenko et al. aging cohorts.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0003/"},
        {"id": "Fig.4", "title": "Shared CPC / NPC programmes", "caption": "Shared DEGs, KEGG pathways and lower aging scores in CEN and offspring T cells.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0004/"},
        {"id": "Fig.5", "title": "SCENIC regulons", "caption": "Longevity-associated TFs including JUND, EOMES, MAFB and FOXO3.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0005/"},
        {"id": "Fig.6", "title": "TCR clonal expansion", "caption": "Lower Shannon diversity, higher clonality and STARTRAC expansion in CEN and offspring.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9799020/figure/advs4471-fig-0006/"}
      ],
      "core_tables": [
        {
          "id": "remodeling-numbers",
          "title": "Published remodeling numbers",
          "source": "PMC9799020 main text.",
          "columns": ["Metric", "Value", "Scope"],
          "rows": [
            ["scRNA samples", "22", "7 CEN + 6 offspring + 9 controls"],
            ["FACS validation n", "30 per group", "CEN / offspring / control"],
            ["CD8 share of CPC in CEN", "~80%", "scRNA T-cell compartment"],
            ["CD4+ CTL mean in CEN", "12.7% of T cells", "Authors contrast with 25.3% in a supercentenarian report"],
            ["Shared CPC DEGs, CEN ∩ offspring", "~40%", "Versus control"],
            ["Enriched CD8 states in CEN/CO", "GZMB+ and CMC1+", "Not a further GZMK+ expansion"],
            ["TCR diversity", "Decreased in CEN and offspring", "Shannon entropy"],
            ["TCR clonality / STARTRAC", "Increased in CEN and offspring", "Clonal expansion"]
          ]
        }
      ],
      "supplements": [
        "Figs S1–S7 (clinical, QC, markers, pathways, TCR, V/J, batch)",
        "Supplemental Tables 1–2"
      ]
    },
    "necs-multimodal-2023": {
      "dataset_id": "necs-multimodal-2023",
      "label": "New England Centenarian multi-modal atlas ('elite immunity')",
      "journal": "eBioMedicine",
      "year": "2023",
      "pmid": "37005201",
      "pmcid": "PMC10114155",
      "doi": "10.1016/j.ebiom.2023.104514",
      "license": "CC BY-NC-ND 4.0",
      "license_note": "Non-derivative licence. Show original figures via PMC; do not redraw UMAPs. Numeric facts below are transcribed from the paper.",
      "access": {
        "status": "tbd",
        "status_label": "NECS Synapse pending · GEO TBD",
        "raw_summary": "Paper text: NECS 'will be available from Synapse'. Public reuse: NATGEN molgenis and RIKEN SC2018. Analysis scripts are on GitHub. No local NECS matrix on LACA.",
        "local_matrix": false,
        "accessions": [
          {"id": "Synapse UH2AG064704", "kind": "Synapse project", "role": "Promised NECS deposit", "url": "https://adknowledgeportal.synapse.org/Explore/Projects/DetailsPage?Grant%20Number=UH2AG064704"},
          {"id": "GitHub sc_pbmc_centenarians", "kind": "code", "role": "Scripts to reproduce figures", "url": "https://github.com/Integrative-Longevity-Omics/sc_pbmc_centenarians"},
          {"id": "NATGEN molgenis", "kind": "public scRNA", "role": "Public lifespan reuse", "url": "https://molgenis58.target.rug.nl/scrna-seq/"},
          {"id": "RIKEN SC2018", "kind": "project page", "role": "Japan public reuse", "url": "http://gerg.gsc.riken.jp/SC2018/"}
        ]
      },
      "links": {
        "pubmed": "https://pubmed.ncbi.nlm.nih.gov/37005201/",
        "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10114155/",
        "article": "https://doi.org/10.1016/j.ebiom.2023.104514"
      },
      "sample_splits": [
        {"site": "Integrated atlas", "cen": 14, "off": 0, "ctl": 52, "note": "66 people / 102,284 cells; EL = 100–119 y"},
        {"site": "New NECS 10x", "cen": 7, "off": 0, "ctl": 2, "note": "16,082 PBMCs; Table 1"}
      ],
      "age_groups": [
        {"label": "Younger 20–39", "n": 12},
        {"label": "Middle 40–59", "n": 26},
        {"label": "Older 60–89", "n": 14},
        {"label": "EL 100–119", "n": 14}
      ],
      "figures": [
        {"id": "Fig.1", "title": "Immune landscape at single-cell resolution", "caption": "UMAP of 102,284 PBMCs from 66 people, labelled by subtype and by four age groups.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10114155/figure/fig1/"},
        {"id": "Fig.2", "title": "Repertoire shifts in extreme longevity", "caption": "Cell-type proportions, diversity statistic (F-test P=0.0001875) and age-coefficient heatmap.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10114155/figure/fig2/"},
        {"id": "Fig.3", "title": "Lymphoid / myeloid resilience hierarchy", "caption": "Average proportions along the peripheral immune hierarchy across four age groups.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10114155/figure/fig3/"},
        {"id": "Fig.4", "title": "Three gene-expression patterns", "caption": "Aging-related, EL-specific and aging-specific DEGs (151 age/EL genes; 387 EL vs younger).", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10114155/figure/fig4/"}
      ],
      "core_tables": [
        {
          "id": "table1",
          "title": "Table 1. New NECS samples (de-identified age range + sex)",
          "source": "Table 1, PMC10114155.",
          "columns": ["Sample ID", "Age range", "Sex"],
          "rows": [
            ["EL1", "100–105", "Male"],
            ["EL2", "105+", "Female"],
            ["EL3", "105+", "Female"],
            ["EL4", "100–105", "Female"],
            ["EL5", "105+", "Male"],
            ["EL6", "105+", "Male"],
            ["EL7", "100–105", "Female"],
            ["YA1", "44", "Male"],
            ["YA2", "34", "Female"]
          ]
        },
        {
          "id": "composition",
          "title": "Published composition contrasts (EL vs younger)",
          "source": "Main text of PMC10114155.",
          "columns": ["Metric", "Younger / 20–89", "Extreme longevity"],
          "rows": [
            ["Myeloid / lymphoid", "13.8% / 86.2%", "25.2% / 74.8%"],
            ["Mono / DC", "85.59% / 14.41%", "94.58% / 5.42%"],
            ["Cytotoxic / non-cytotoxic lymphocytes", "30.30% / 69.70%", "70.94% / 29.06%"],
            ["Non-cytotoxic: CD4 T / B", "90.86% / 9.41%", "81.55% / 18.45%"],
            ["CD4 T: memory / naive", "39.46% / 60.54%", "65.72% / 34.28%"],
            ["cCD4TC share of PBMCs", "<1%", "7.5% male EL; 6.0% female EL"],
            ["Integrated n people / cells", "—", "66 / 102,284"],
            ["DEG EL vs younger", "—", "387 (136 up / 251 down)"]
          ]
        }
      ],
      "cell_types_12": ["nCD4TC", "mCD4TC", "cCD4TC", "cCD8TC", "nBC", "mBC", "gdTC", "NK", "M14", "M16", "mDC", "pDC"],
      "supplements": [
        "mmc1.pptx — supplementary figures (8.1 MB)",
        "mmc2.pdf — supplementary text (166 KB)",
        "mmc3.xlsx — supplementary tables S3, S7–S29 (345 KB)"
      ]
    },
    "longevity-molecular-tag-2026": {
      "dataset_id": "longevity-molecular-tag-2026",
      "label": "'Longevity Molecular Tag' immune-cell atlas",
      "journal": "Aging Cell",
      "year": "2026",
      "pmid": "41784043",
      "pmcid": "PMC12961527",
      "doi": "10.1111/acel.70431",
      "license": "CC BY 4.0",
      "license_note": "Open licence. Captions and published numbers may be shown with attribution. Underlying scRNA is reused from Synapse / RIKEN, not generated as a new open GEO series.",
      "access": {
        "status": "tbd",
        "status_label": "Public reuse · not local",
        "raw_summary": "56-person East-Asian scRNA reused from Synapse syn61609846 (doi 10.1038/s41590-024-02059-6). Japan 7 SC + 5 controls from RIKEN SC2018. Guangxi bulk: 34 centenarians + 16 controls. No local matrix on LACA.",
        "local_matrix": false,
        "accessions": [
          {"id": "syn61609846", "kind": "Synapse", "role": "56-person scRNA reuse", "url": "https://www.synapse.org/#!Synapse:syn61609846"},
          {"id": "RIKEN SC2018", "kind": "project page", "role": "7 supercentenarians + 5 controls", "url": "http://gerg.gsc.riken.jp/SC2018/"},
          {"id": "NCT05206643", "kind": "ClinicalTrials.gov", "role": "Related trial record", "url": "https://clinicaltrials.gov/study/NCT05206643"},
          {"id": "eQTLGen sc", "kind": "summary stats", "role": "cis-eQTL used for colocalisation", "url": "https://eqtlgen.org/sc/"}
        ]
      },
      "links": {
        "pubmed": "https://pubmed.ncbi.nlm.nih.gov/41784043/",
        "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/",
        "article": "https://doi.org/10.1111/acel.70431"
      },
      "sample_splits": [
        {"site": "East-Asian scRNA (Shanghai reuse)", "cen": 0, "off": 0, "ctl": 56, "note": "Ages 0 to ≥90; Synapse syn61609846"},
        {"site": "Japan SC2018", "cen": 7, "off": 0, "ctl": 5, "note": "Supercentenarians + controls"},
        {"site": "Guangxi bulk RNA-seq", "cen": 34, "off": 0, "ctl": 16, "note": "Control mean age 52.81 ± 9.78"}
      ],
      "figures": [
        {"id": "Fig.1", "title": "Aging-cohort transcriptome landscape", "caption": "UMAP of 9 lineages and 21 subpopulations; proportions across age groups. 559,713 cells after QC.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/figure/acel70431-fig-0001/"},
        {"id": "Fig.2", "title": "Scissor+ / Scissor− map", "caption": "13,198 Scissor+ vs 18,075 Scissor− vs 21,328 background cells among 52,601 analysed cells.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/figure/acel70431-fig-0002/"},
        {"id": "Fig.3", "title": "Lineage trajectories", "caption": "NK, CD8, CD4 and B subpopulations with pseudotime.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/figure/acel70431-fig-0003/"},
        {"id": "Fig.4", "title": "DEG and enrichment", "caption": "317 up / 147 down DEGs between Scissor+ and Scissor−, with GO / KEGG.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/figure/acel70431-fig-0004/"},
        {"id": "Fig.5", "title": "Longevity eQTL colocalisation", "caption": "Five events with PP.H4 > 0.7, including rs3793537 and rs8019902.", "pmc": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12961527/figure/acel70431-fig-0005/"}
      ],
      "core_tables": [
        {
          "id": "scissor",
          "title": "Scissor and DEG counts",
          "source": "PMC12961527 results.",
          "columns": ["Item", "N", "Note"],
          "rows": [
            ["Cells after QC", "559,713", "5,402 excluded"],
            ["Cells in Scissor analysis", "52,601", "Subset used for phenotype link"],
            ["Scissor+", "13,198", "NK, CD8, γδ T enriched"],
            ["Scissor−", "18,075", "CD4, B, DC enriched"],
            ["Background", "21,328", "Neither pole"],
            ["DEGs up / down", "317 / 147", "464 total"],
            ["Uniquely expressed in centenarians", "441", "Bulk / integration overlay"]
          ]
        },
        {
          "id": "eqtl",
          "title": "eQTL colocalisation (PP.H4 > 0.7)",
          "source": "Main text + Table S10. Remaining three events are named only in the supplement.",
          "columns": ["SNP", "Genes", "Locus note"],
          "rows": [
            ["rs3793537", "GLIPR2 / CD72 / TLN1", "chr9; named in abstract and Fig.5"],
            ["rs8019902", "TRDV2 / TRDC", "chr14; named in abstract and Fig.5"],
            ["3 further events", "see Table S10", "PP.H4 > 0.7; not numerically expanded in the main text"]
          ]
        }
      ],
      "lineages_9": ["CD4+ T", "CD8+ T", "γδ T", "NK", "B", "DC", "Monocyte", "Megakaryocyte", "Erythrocyte"],
      "supplements": [
        "Figs S1–S4 (QC, 42 markers, marker-by-cell-type, marker-by-age)",
        "Tables S1–S10 (baseline, Scissor proportions, DEGs, GO/KEGG, eQTL events)"
      ]
    }
  }
}