datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
bio-mcp-data
Bio-MCP-Data
A repository containing biological datasets that will be used by BIO-MCP MCP (Model Context Protocol) standard.
About
This repository hosts biological data assets formatted to be compatible with the Model Context Protocol, enabling AI models to efficiently access and process biological information. The data is managed using Git Large File Storage (LFS) to handle large biological datasets.
Purpose
Provide standardized biological datasets for AI… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/bio-mcp-data.gene-expression-single-cell-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.
Data Files
This dataset contains multiple parquet files, one for each sheet in the original Excel file:
gene-expression-single-cell-mouse_*.parquet - Data files containing gene expression and… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/gene-expression-single-cell-mouse.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.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.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.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.cellxgene_standard
Cellxgene Human Aging Meta Summary
A curated summary of human single-cell RNA-seq datasets from cellxgene, focused on aging and development, with standardized metadata across experiments and assays.
Intended Use
This summary is intended as a scaffold for integrating other curated or custom single-cell datasets (e.g., aging or disease-focused studies) with Cellxgene metadata. Enables exploration, QC, and pre-integration filtering at the experiment level. The seafront… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/cellxgene_standard.my_datasetaging-fly-cell-atlas
🧬 Aging Fly Cell Atlas (AFCA) - Complete Dataset
Comprehensive single-nucleus transcriptomic atlas of aging in Drosophila melanogaster covering both head and body tissues for longevity research and machine learning applications
📊 Dataset Overview
Original Study: Lu et al., Science 2023Interactive Atlas: hongjielilab.org/afcaGEO Repository: GSE218661Processing Repository: github.com/winternewt/aging-fly-cell-atlas - Complete data processing pipeline
This dataset… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/aging-fly-cell-atlas.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.skeletal-muscle-atlas
🧬 Human Skeletal Muscle Aging Atlas - 10X Chromium Dataset
A comprehensive single-cell RNA-seq atlas of human skeletal muscle aging across the lifespan (15-75 years)
Skeletal muscle aging is characterized by progressive loss of muscle mass and strength, often leading to sarcopenia and frailty in older adults. This dataset originates from the Human Skeletal Muscle Aging Atlas study published in Nature Aging (2024), which provides molecular insights into how aging affects different… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/skeletal-muscle-atlas.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.cell2sentence4longevity-opengenes-datapan-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.atomica_longevity_proteins
Longevity Protein Structures Dataset
Quick Start
# Load the dataset index
from datasets import load_dataset
ds = load_dataset("longevity-genie/atomica_longevity_proteins")
# Or use Polars directly
import polars as pl
df = pl.read_parquet("hf://datasets/longevity-genie/atomica_longevity_proteins/atomica_index.parquet")
# Find KEAP1 structures
keap1 = df.filter(pl.col("gene_symbols").list.contains("KEAP1"))
print(f"Found {len(keap1)} KEAP1 structures")… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/atomica_longevity_proteins.mouse-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.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.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.aging-expressions
aging-expressions: Age-Stratified Gene Expression Dataset
Dataset Description
This dataset provides age-stratified gene expression data derived from ARCHS4 and GTEx databases, specifically curated for fine-tuning BulkFormer and other bulk RNA-seq deep learning models. The dataset contains TPM-normalized expression values for protein-coding genes, enriched with comprehensive demographic metadata including precise age information.
Key Features:
🎯 Optimized for BulkFormer:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-genie/aging-expressions.snRNAseq_of_human_optic_nerve_and_optic_nerve_head_endothelial_cells
Human Optic Nerve Endothelial Cells (snRNA-seq) Dataset
Dataset Overview
This dataset comprises single-nucleus RNA sequencing (snRNA-seq) data specifically focusing on endothelial cells from the human optic nerve and optic nerve head. It represents a valuable resource for investigating cell-type specific gene expression profiles within a critical ocular tissue.
The data was sourced from the CZ CELLxGENE Discover API, providing access to a deeply characterized single-cell… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/snRNAseq_of_human_optic_nerve_and_optic_nerve_head_endothelial_cells.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.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.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.tissue_cell_raw_p_dataset_new
Tissue Cell Raw P Dataset
This dataset was processed using the parq2hug tool on 2025-06-15.
Dataset Information
Rows: 20,116
Columns: 195
File Size: 25.91 MB
File Structure
expression.parquet
expression.parquet contains the main dataset with 20,116 rows and 195 columns.
feature_metadata.parquet
feature_metadata.parquet contains metadata for each feature (column) in the dataset, including:
Feature name
Data type
Statistics (count, mean… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/tissue_cell_raw_p_dataset_new.tissue_cell_raw_p_dataset
Tissue Cell Raw P Dataset
This dataset was processed using the parq2hug tool on 2025-06-15.
Dataset Information
Rows: 20,116
Columns: 195
File Size: 25.91 MB
File Structure
expression.parquet
expression.parquet contains the main dataset with 20,116 rows and 195 columns.
feature_metadata.parquet
feature_metadata.parquet contains metadata for each feature (column) in the dataset, including:
Feature name
Data type
Statistics (count, mean… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/tissue_cell_raw_p_dataset.tissue-cell-raw-p-datasetThis data was collected from the Nature publication
"A single-cell transcriptomic atlas characterizes ageing tissues in the mouse"
DOI: https://doi.org/10.1038/s41586-020-2496-1
Gene Expression Omnibus (GEO) Accession Code: GSE132042
In this study, researchers looked at how much certain genes were expressed in
young and old mice so that they could compare gene expression between the groups.
This provides data on how gene expression changes with age. Specifically, the
samples were taken from… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/tissue-cell-raw-p-dataset.terekhova2023
Dataset Card for tereshkova2023_processed
Dataset Summary
This dataset is a single-cell multi-omic atlas of peripheral blood mononuclear cells (PBMCs) from 166 healthy donors aged 25–85, comprising ~2 million cells profiled with scRNA-seq, TCR/BCR-seq, and surface protein barcoding (CITE-seq). It supports cell type annotation, immune aging trajectory modeling, and multimodal integration. It is described in:
Single-cell atlas of healthy human blood unveils age-related… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/terekhova2023.sc-ImmuAging
🧬 sc-ImmuAging – Human PBMC Single-Cell Aging Clock Dataset
This dataset includes curated feature selections from peripheral blood mononuclear cells (PBMCs) used to train aging clock models across five major immune cell types. It was derived from the sc-ImmuAging project to understand how aging affects the immune system at the single-cell level using machine learning models.
📦 Dataset Contents
sc-ImmuAging.parquet — Long-format data containing gene features per immune… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/sc-ImmuAging.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.cultured_meat_paragraphs