Archive of OMICS databases with open datasets

A searchable table of periodically updated and daily tested OMICS databases with open access datasets.

In this notebook, we provide a searchable table of periodically updated and daily tested OMICS databases with open access datasets. The table is based on multiple online sources and inputs from our colleagues and ABC participants. The links are tested automatically every day at midnight, and an error in opening the related webpage is signaled in the table. When we verify the malfunctioning of the link, we remove the database from the list after a reasonable grace period.

Note

For any contribution or suggestion, please contact us at abcafe [at] au.dk, or open an issue on the Github repository of this webpage. Any input is considered, especially if you produced your own database and want to share it with the community!!!

ⓘName	Description	Organism	Organ	Format	Type	Link	Tested	Date_tested
Gene Expression Omnibus (GEO)	Public functional genomics data repository	Many	Many	short-read seq, long-read seq	processed	<a href="https://www.ncbi.nlm.nih.gov/geo/">LINK</a>	Working	2026-08-14
Sequence Read Archive (SRA)	Raw sequencing data and alignment information from GEO datasets	Many	Many	short-read seq, long-read seq	raw	<a href="https://www.ncbi.nlm.nih.gov/sra/">LINK</a>	Working	2026-08-14
Human Brain Transcriptome	Transcriptome data and associated metadata for the developing and adult human brain	Human	Brain	transcriptomics, Affymetrix Chip, Genotype (request)	raw, processed	<a href="https://hbatlas.org/">LINK</a>	Working	2026-08-14
Allen brain atlas	A wide set of tools and data focused on the brain	Human, Mouse, Primates	Brain	scRNA, imaging, RNA, microarray, spatial, ISH	raw, processed	<a href="https://portal.brain-map.org/">LINK</a>	Working	2026-08-14
BrainSpan	Foundational resource for studying transcriptional mechanisms involved in human brain development.	Human	Brain	RNA, microarray, anatomic imaging, ISH	raw, processed	<a href="https://www.brainspan.org/">LINK</a>	Working	2026-08-14
EnrichR	Website/interactive and collaborative gene list enrichment tool using ARCHS4	Human, Mouse	Many	Web Tool	processed	<a href="https://maayanlab.cloud/Enrichr/">LINK</a>	Working	2026-08-14
SysNDD	Gene disease relationships in neurodevelopmental disorders (NDD)	Human	Brain	Web Tool	processed	<a href="https://sysndd.dbmr.unibe.ch/">LINK</a>	Working	2026-08-14
Adult Genotype Tissue Expression (GTEx)	Tissue and cell-specific gene expression and regulation across individuals, development, and species	Human, Primates	Many	scRNA, RNA, QTL, Chip-seq, Metilation, Biobank (request)	processed	<a href="https://gtexportal.org/home/">LINK</a>	Working	2026-08-14
Human protein atlas	The open access resource for human proteins	Human	Many	scRNA, RNA, protein concentration, protein-protein interaction	raw, processed	<a href="https://www.proteinatlas.org/">LINK</a>	Working	2026-08-14
FANTOM	Functional elements in mammalian genomes	Many	Many	transcriptomics	raw, processed	<a href="https://fantom.gsc.riken.jp/">LINK</a>	Working	2026-08-14
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