Curated public single-cell / single-nucleus and spatial transcriptomics datasets for human (and one mouse) testis, placenta, and brain (development · Parkinson's · Alzheimer's · normal). Used as the raw input for cross-tissue cancer-testis-antigen (CTA) analysis.

⚠️ Public data, mirrored for research. Every file was downloaded from public, open-access sources (CZ CELLxGENE Discover; NCBI GEO supplementary). No controlled-access data, no PII. Each dataset retains its ORIGINAL source license — cite the original study and follow its terms.

At a glance

Files: 30 data files (+ README.md, _manifest.csv, .gitattributes)
Total size: 37.67 GB (35.08 GiB)
Integrity: every large file is Git-LFS tracked with a sha256 checksum (HF verifies on download); 0 empty files.
Authoritative per-file metadata: _manifest.csv (one row per file).

By tissue

tissue	files	size
brain	10	18.58 GB
placenta	12	10.40 GB
testis	8	8.69 GB

By modality

modality	files	size
scRNA-seq	14	24.59 GB
snRNA-seq	1	4.99 GB
spatial	15	8.09 GB

Full file manifest

file	tissue	modality	condition	accession	approx cells	size
`brain/scRNA_AD/AD_brain_vascular_65k.h5ad`	brain	scRNA-seq	Alzheimer's disease (AD)	CZ CELLxGENE	~65,000	628 MB
`brain/scRNA_AD/AD_tangle_bearing_neurons_96k.h5ad`	brain	scRNA-seq	Alzheimer's disease (AD)	CZ CELLxGENE	~96,000	1256 MB
`brain/scRNA_AD/SEA-AD_AllCells_snRNA_432k.h5ad`	brain	snRNA-seq	Alzheimer's disease (AD)	CZ CELLxGENE	~432,000	4994 MB
`brain/scRNA_PD/PD_Astrocytes_33k.h5ad`	brain	scRNA-seq	Parkinson's disease (PD)	CZ CELLxGENE	~33,000	233 MB
`brain/scRNA_PD/PD_NonDA_Neurons_91k.h5ad`	brain	scRNA-seq	Parkinson's disease (PD)	CZ CELLxGENE	~91,000	1192 MB
`brain/scRNA_PD/PD_Oligodendrocytes_179k.h5ad`	brain	scRNA-seq	Parkinson's disease (PD)	CZ CELLxGENE	~179,000	1084 MB
`brain/scRNA_development/Dev_prenatal_postnatal_cortex_709k.h5ad`	brain	scRNA-seq	development	CZ CELLxGENE	~709,000	5976 MB
`brain/spatial_AD/GSE308007_AD_entorhinal_spatial_sc.tar`	brain	spatial	Alzheimer's disease (AD)	GSE308007	—	2099 MB
`brain/spatial_PD/GSE253975_PD_substantia_nigra_Visium_ST.tar`	brain	spatial	Parkinson's disease (PD)	GSE253975	—	21 MB
`brain/spatial_development/GSE277032_fetal_midbrain_spatiotemporal.tar`	brain	spatial	development	GSE277032	—	1094 MB
`placenta_development/scRNA/All_cell_states_maternal_fetal.h5ad`	placenta	scRNA-seq	development	CZ CELLxGENE	—	3603 MB
`placenta_development/scRNA/Placenta_Infection_Carnegie9-23.h5ad`	placenta	scRNA-seq	infection	CZ CELLxGENE	—	5023 MB
`placenta_development/scRNA/Trophoblast_Organoids.h5ad`	placenta	scRNA-seq	normal/development	CZ CELLxGENE	—	1082 MB
`placenta_development/spatial_early_visium/PS1_WS_PLA_S9101764_wk9.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	43 MB
`placenta_development/spatial_early_visium/PS2_WS_PLA_S9101765_wk9.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	43 MB
`placenta_development/spatial_early_visium/PS3_WS_PLA_S9101766_wk9.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	35 MB
`placenta_development/spatial_early_visium/PS4_WS_PLA_S9101767_wk9.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	45 MB
`placenta_development/spatial_early_visium/PS5_Pla_Camb9518737_wk9.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	41 MB
`placenta_development/spatial_early_visium/PS6_Pla_HDBR_Carnegie18.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	26 MB
`placenta_development/spatial_early_visium/PS7_WS_PLA_S9101769_Carnegie23.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	38 MB
`placenta_development/spatial_early_visium/PS8_WS_PLA_S9101770_Carnegie23.h5ad`	placenta	spatial	normal/development	CZ CELLxGENE	—	39 MB
`placenta_development/spatial_term_visium/GSE222987_term_placenta_Visium.tar`	placenta	spatial	normal/development	GSE222987	—	387 MB
`testis_development/scRNA/Human_Germ_Cells_PGC.h5ad`	testis	scRNA-seq	normal/development	CZ CELLxGENE	—	197 MB
`testis_development/scRNA/Human_Male_gonad.h5ad`	testis	scRNA-seq	normal/development	CZ CELLxGENE	—	1302 MB
`testis_development/scRNA/Human_Somatic_Lineage.h5ad`	testis	scRNA-seq	normal/development	CZ CELLxGENE	—	2245 MB
`testis_development/scRNA/Human_fetal_gonad_wk11-16.h5ad`	testis	scRNA-seq	development	CZ CELLxGENE	—	380 MB
`testis_development/scRNA/TabulaSapiens_Testis_adult.h5ad`	testis	scRNA-seq	normal/development	CZ CELLxGENE	—	385 MB
`testis_development/spatial/Chen2021_human_mouse_testis_SlideseqV2.zip`	testis	spatial	normal/development	—	—	225 MB
`testis_development/spatial/GSE244586_mouse_testis_spatial.tar`	testis	spatial	normal/development	GSE244586	—	4 MB
`testis_development/spatial/GSE307496_bovine_testis_Stereoseq.tar`	testis	spatial	normal/development	GSE307496	—	3946 MB

approx cells is parsed from the filename where the author encoded it (e.g. …_432k); spatial .tar bundles contain per-spot/segment matrices rather than a single cell count.

Provenance

CZ CELLxGENE Discover — analysis-ready .h5ad (testis germ/somatic, placenta trophoblast & maternal–fetal interface, developing & diseased brain).
NCBI GEO supplementary — spatial bundles (.tar): Visium / Slide-seq / Stereo-seq / GeoMx DSP. Accessions are embedded in the filenames (column accession of _manifest.csv).

Each dataset retains the license of its source repository / original publication.

How to use

from huggingface_hub import hf_hub_download
import anndata as ad
p = hf_hub_download("wei82/omics-dev-data", repo_type="dataset",
                    filename="brain/scRNA_PD/PD_Astrocytes_33k.h5ad")
adata = ad.read_h5ad(p, backed="r")     # backed='r' = read metadata without loading into RAM
print(adata)

Spatial .tar files: download, tar -xf, then read the enclosed matrices (Visium filtered_feature_bc_matrix, Slide-seq beads, Stereo-seq bins, or GeoMx .dcc/PKC) with scanpy / squidpy.

Finding / matching analyses

Analyses derived from this data are recorded in the matching private analysis repo (wei82/omics-dev-results) keyed by dataset id — so any result maps back to the exact file here.

Disclaimer

Research convenience mirror; not affiliated with the original data providers. Verify each dataset's original license before reuse or redistribution.

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