GEOMeta: Large-Scale Human Bulk RNA-seq Dataset with Curated Metadata

Overview

GEOMeta is a large-scale human bulk RNA-seq dataset derived from the ARCHS4 resource, containing transcript abundance profiles for ~474,000 samples across training, test, and held-out test splits. Each sample is annotated with standardized metadata including sex, organ system, disease category, age group, and experimental setting.

Dataset Construction

Transcript abundance profiles were obtained from the ARCHS4 human reference HDF5 file (human_gene_v2.5.h5). Genes were read in batches of 1,000 per chunk to reduce memory usage, with two known problematic gene index ranges (indices 56,000–58,000) excluded. Gene identifiers (Ensembl ID, gene symbol) and sample annotations (GSM accession, sample name, series ID) were extracted from the same HDF5 file and assembled into an AnnData object.

Curated metadata tables were then merged by GSM accession to add standardized attributes. Duplicate GSM entries were removed (keeping first occurrence).

The script used to generate the AnnData files is provided at data/generate_h5ad.py.

Files

File	Description	Samples
data/human_gene_v2.5_train_nhmerged.h5ad	Training split	~436,000
data/human_gene_v2.5_test_nhmerged.h5ad	Test split	~24,500
data/human_gene_v2.5_test_2024_nhmerged.h5ad	Held-out test split (2024 samples)	~13,600
data/GEO_HUMAN_500K_training.csv	Metadata for training split	~436,000
data/GEO_HUMAN_500K_test.csv	Metadata for test split	~24,500
data/GEO_HUMAN_500K_test_2024.csv	Metadata for held-out test split	~13,600
data/generate_h5ad.py	Script to reproduce AnnData files from source HDF5	—

AnnData Structure

.obs (sample-level metadata)

Field	Description
geo_accession	GSM accession ID
sample	Sample name
series_id	GSE series ID
gender	Sex (standardized)
organ_system	Organ/tissue system
disease	Disease label (Normal for healthy samples)
age	Age group
Experimental_Setting	Experimental context (e.g., In Vitro, In Vivo)
Broad_Disease_Category	Broad disease category (grouped from disease)

.var (gene-level metadata)

Field	Description
ensembl_id / ensembl.gene	Ensembl gene ID (index)
symbol	Gene symbol

.X

Raw transcript abundance matrix (samples × genes), sparse format. Gene coverage spans 65,186 genes (67,186 total minus the 2,000 excluded problematic indices).

Metadata CSV Columns

Column	Description
GSE_ID	GEO Series accession
GSM_ID	GEO Sample accession
year	Year of submission
contact_country	Submitting country
instrument_model	Sequencing platform
RNA_Library	Library type (e.g., mRNA-based)
Exp_Setting	Experimental setting
GSE_Pert	Whether the series involves a perturbation
Disease	Disease label
Organ	Organ/tissue
Gender	Sex
Age_Group	Age group

Usage

import anndata as ad

adata_train = ad.read_h5ad("data/human_gene_v2.5_train_nhmerged.h5ad")
adata_test  = ad.read_h5ad("data/human_gene_v2.5_test_nhmerged.h5ad")
adata_test_2024 = ad.read_h5ad("data/human_gene_v2.5_test_2024_nhmerged.h5ad")

print(adata_train)
# AnnData object with n_obs × n_vars = ~436000 × 65186

Source

• ARCHS4: https://maayanlab.cloud/archs4/
• Raw HDF5 file: human_gene_v2.5.h5 (available from ARCHS4)