Datasets:

wei82
/

omics-dev-data

---

pretty_name: Testis / Placenta / Brain Development — single-cell & spatial (multi-omics)
license: other
language:
- en
tags:
- biology
- single-cell
- spatial-transcriptomics
- developmental-biology
- testis
- placenta
- brain
- neurodegeneration
- genomics
viewer: false
size_categories:
- 1M<n<10M
---


# Testis / Placenta / Brain Development — single-cell & spatial (multi-omics)

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`](./_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
```python

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.