datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
aging-gene-expression-single-cell-mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
https://www.nature.com/articles/s41586-020-2496-1#Sec2
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Dataset structure is originally from AnnData.
Descriptions of each data file is below.
Data Files
This dataset contains multiple parquet files, one for each sheet in the original Excel file:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/aging-gene-expression-single-cell-mouse.cell2sentence4longevity-data
Dataset Card: longevity-genie/cell2sentence4longevity-data
Summary
This repository contains preprocessed single-cell RNA-seq (scRNA‑seq) datasets prepared as “cell sentences” for training and evaluation of cells2sentence-style models. Each cell is represented as a space‑separated sequence of top expressed gene symbols, enabling language‑model style training for tasks such as biological age prediction and other downstream applications.
This dataset targets fine‑tuning and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/cell2sentence4longevity-data.tabula-muris-senis-bladder-smartseq2
Bladder Tissue from Tabula Muris Senis
Tabula Muris Senis is a mammalian aging single-cell gene expression dataset, downloaded from https://cellxgene.cziscience.com/collections/0b9d8a04-bb9d-44da-aa27-705bb65b54eb. This dataset represents the Bladder tissue, using the SmartSeq2 full-length mRNA library preparation method for single cells.
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Ageing is characterized by a… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/tabula-muris-senis-bladder-smartseq2.Tabula_Muris_Senis_10x
🧬 Tabula Muris Senis – 10x Dataset (Mouse Aging Atlas)
Organism: Mus musculusAssay: 10x Genomics Single Cell 3' v2Tissues: 16 mouse tissues (e.g., heart, lung, kidney, liver)Cells: 245,000+ single cellsAge groups: Spanning mouse lifespan (young to old)
📖 Dataset Description
This dataset is a subset of the Tabula Muris Senis project, a collaborative effort to create a comprehensive single-cell transcriptomic atlas of aging in the mouse. The 10x portion of the data… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/Tabula_Muris_Senis_10x.human-muscle-aging-atlas-snRNAseq
Human Skeletal Muscle Aging Atlas (sn/scRNA-seq) Dataset
1. Data Overview
This dataset provides single-nucleus and single-cell RNA sequencing (sn/scRNA-seq) data specifically focusing on the human skeletal muscle across different age groups. It serves as a rich resource for investigating cell-type specific gene expression changes and cellular composition shifts that occur during the aging process in a critical human tissue.
The original data was sourced from the Human… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/human-muscle-aging-atlas-snRNAseq.cell2sentence4longevity-opengenes-datamouse-muscle-aging-atlas-snRNAseq
Mouse Skeletal Muscle Aging Atlas (sn/scRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus and single-cell RNA sequencing (sn/scRNA-seq) data specifically focusing on the mouse skeletal muscle across different age groups. It serves as a valuable resource for investigating cell-type-specific gene expression changes and cellular composition shifts that occur during the aging process in a crucial mammalian model system.
The data was sourced from the… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/mouse-muscle-aging-atlas-snRNAseq.ainciburu2023
Dataset Card for ainciburu_processed
Dataset Summary
This dataset comprises ~115,000 CD34+ hematopoietic stem and progenitor cells (HSPCs) profiled via 10x Genomics single-cell RNA-seq from healthy young, elderly, and myelodysplastic syndrome (MDS) patients. The data originates from:
Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single-cell resolution— Ainciburu et al., eLife (2023)PMCID: PMC9904760DOI:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/ainciburu2023.transcriptomic-atlas-mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Dataset structure is originally from AnnData.
Descriptions of each data file is below.
transcriptomic-atlas-mouse_expression.parquet
The main expression matrix containing gene expression data.
transcriptomic-atlas-mouse_sample_metadata.parquet
Metadata for each… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/transcriptomic-atlas-mouse.cleaned_data
Cleaned Tabula Muris Senis Single-Cell Data and other aging datasets
This dataset contains LLM-cleaned single-cell transcriptomic annotations from the Tabula Muris Senis project, specifically for mouse tissues processed with SmartSeq2, and ALL OTHER DATASETS WITH AGING IN THE FILENAME :-) . The cleaning and annotation were performed using large language models (OpenAI and Claude), enabling enriched metadata and corrected cell type labels.
🧬 Over 1.3 million rows and 78.17 GB… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/cleaned_data.bio-faiss-longevity-v1
bio-faiss-longevity-v1
A FAISS index + metadata for scientific retrieval
Contents
index.faiss: FAISS index (cosine w/ inner product).
meta.jsonl: one JSON per chunk; fields include chunk_id, paper_id, title, section, subsection, paragraph_index, keywords, boost.
index.info.json: (optional) dimensions, index type, faiss version.
Build provenance
Chunking: hierarchical (section→paragraph→~480-token chunks, ~15% overlap)
Embedder:… See the full description on the dataset page: https://huggingface.co/datasets/bio-protocol/bio-faiss-longevity-v1.riken2018
Dataset Card for riken2018_processed
Dataset Summary
This dataset is derived from single-cell RNA-seq of peripheral blood mononuclear cells (PBMCs) from supercentenarians (ages 110+) and younger controls, processed from the study:
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians— Hashimoto et al., PNAS (2019)DOI:10.1073/pnas.1907883116
The final object includes cells from three experimental batches (firstrun, SC1, SC2) and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/riken2018.human-cornea-snRNAseq
Human Cornea Atlas (snRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus RNA sequencing (snRNA-seq) data specifically focusing on the cellular heterogeneity of the human cornea. It provides a high-resolution view of various cell populations and their gene expression profiles across different layers of this critical ocular tissue.
The data was sourced from a research paper providing a comprehensive single-cell transcriptome atlas of the human cornea.… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/human-cornea-snRNAseq.pan-cancer-nuclei-seg
Nuclear Aging Morphometry Dataset: TCGA Bladder Cancer Nuclei Features for Longevity Research
Dataset Description
This dataset provides nuclear morphometric features extracted from TCGA bladder cancer histopathology slides, specifically designed for aging and longevity research. The dataset contains quantitative shape measurements of >1M individual nuclei across multiple fields of view, enabling machine learning approaches to study cellular aging, senescence biomarkers… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/pan-cancer-nuclei-seg.sc-human-blood-aging-atlas
sc-human-blood-aging-atlas
Study Description
This dataset accompanies the study “Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB− CD8+ memory T cells and accumulation of type 2 memory CD4+/CD8+ T cells”, which provides a comprehensive single-cell transcriptomic and proteomic landscape of peripheral blood from healthy individuals across the adult lifespan.
Using single-cell RNA sequencing (scRNA-seq) integrated with TCR/BCR profiling and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/sc-human-blood-aging-atlas.GSE167186
GSE167186 – Single-Nucleus RNA-Seq of Aged Human Skeletal Muscle
Organism: Homo sapiensTissue: Human skeletal muscleSamples: 23 individuals (young and aged)Technique: 10x Genomics single-nucleus RNA-seqData Type: Processed sparse expression matrix and cell metadata
🧭 Description
This dataset contains single-nucleus transcriptomes from human skeletal muscle samples spanning young and aged adult individuals. The goal was to understand the molecular changes in muscle… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/GSE167186.mouse-glioblastoma-snRNAseq
Mouse Glioblastoma Atlas (snRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus RNA sequencing (snRNA-seq) data from the brain (glioblastoma tumors and their microenvironment) of both young and aged mice. It provides a high-resolution cellular and molecular census of glioblastoma, a highly aggressive brain tumor, with crucial insights into its age-related characteristics.
The original data was sourced from a CELLxGENE Discover collection titled… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/mouse-glioblastoma-snRNAseq.Human_Ageing_Genomic_Resources
🧬 Human Ageing Genomic Resources (HAGR)
This dataset collection is derived from the Human Ageing Genomic Resources (HAGR), a curated set of databases focusing on the genetics of human aging, longevity, and cellular senescence. It includes several valuable resources formatted as .parquet files for easy use in data science and machine learning pipelines.
📦 Files Included
drugage.parquet: Database of drugs that affect lifespan in model organisms.
genage_human.parquet:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/Human_Ageing_Genomic_Resources.huberman_lab_Dr__Sara_Gottfried_How_to_Optimize_Female_Hormone_Health_for_Vitality__Longevitycultured_meat_paragraphsGSE208154
GSE208154 – Complete Cell Atlas of Aging C. elegans
📄 Description
This dataset provides a comprehensive single-cell RNA sequencing (scRNA-seq) profile of C. elegans across six adult time points. It is a highly curated developmental and aging atlas, useful for longevity, developmental biology, and transcriptomic studies.
📊 Dataset Summary
Species: Caenorhabditis elegans
Type: Single-cell RNA-seq (scRNA-seq)
Samples: 11 GSM samples from GEO
Format:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/GSE208154.civil-engineering-longevity
Civil Engineering Longevity
Infrastructure durability data for civil engineering.
Usage
from datasets import load_dataset
dataset = load_dataset("infra-durability-proj/civil-engineering-longevity")
df = dataset["train"].to_pandas()
Or use the provided loader:
from loader import load_data
df = load_data()
Schema
Metrics
Column
Type
Description
redundancy_factor
float
Normalized metric
load_distribution
float
Normalized metric… See the full description on the dataset page: https://huggingface.co/datasets/infra-durability-proj/civil-engineering-longevity.huberman_lab_GUEST_SERIES__Dr._Andy_Galpin_Optimize_Your_Training_Program_for_Fitness__Longevityhuberman_lab_Dr__Rhonda_Patrick_Micronutrients_for_Health__Longevitymoskalev_papersAll Alexey Moskalev paper found inside semantic-scholar that have pubmed ids.
The parquet file schema is:
root
|-- corpusid: long (nullable = true)
|-- updated: string (nullable = true)
|-- content_source_oainfo_license: string (nullable = true)
|-- content_source_oainfo_openaccessurl: string (nullable = true)
|-- content_source_oainfo_status: string (nullable = true)
|-- content_source_pdfsha: string (nullable = true)
|-- content_source_pdfurls: array (nullable = true)
| |--… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/moskalev_papers.huberman_lab_Dr__Gabrielle_Lyon_How_to_Exercise__Eat_for_Optimal_Health__Longevityhuberman_lab_Dr__Satchin_Panda_Intermittent_Fasting_to_Improve_Health_Cognition__Longevityhuberman_lab_Dr._Peter_Attia_Exercise_Nutrition_Hormones_for_Vitality__Longevityhuberman_lab_GUEST_SERIES__Dr__Andy_Galpin_Optimize_Your_Training_Program_for_Fitness__Longevitybankless_Longevity__Zuzalu_3