Data Card: accurate sizes (GB+GiB), fix size_categories, add full per-file manifest [audit]

README.md

@@ -1,43 +1,114 @@
----
-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
-- genomics
-viewer: false
-size_categories:
-- n>1T
----
-# Testis / Placenta / Brain Development — single-cell & spatial (multi-omics)
-
-Curated public single-cell and spatial transcriptomics datasets for human testis, placenta, and brain (development / PD / AD / normal), used as the raw input for cancer-testis-antigen (CTA) cross-tissue analysis.
-
-> ⚠️ **Public data, mirrored for research.** Downloaded from public, open-access sources
-> (no controlled-access / no PII). **Each dataset retains its ORIGINAL source license** —
-> cite the original study and follow its terms. Provenance below.
-
-- **Total:** 32 files · 35.08 GB
-
-## Provenance
-- CZ CELLxGENE Discover (scRNA h5ad) — testis germ/somatic, placenta trophoblast & maternal-fetal, brain.
-- NCBI GEO supplementary (spatial Visium / Slide-seq / Stereo-seq).
-- See file names for accessions; each retains its source license.
-
-## Contents (top-level)
-- `(root)/` — 2 files, 0.0 GB
-- `brain/` — 10 files, 17.3 GB
-- `placenta_development/` — 12 files, 9.7 GB
-- `testis_development/` — 8 files, 8.1 GB
-
-## Finding / matching data
-Browse by folder above. Analyses derived from this data are recorded in the matching
-**private** analysis repo's `analysis_index.csv` (keyed by dataset id) — so you can map any
-analysis result back to the exact dataset(s) here.
+---
+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.