# Single-nucleus atlas provenance

The two cardiac single-nucleus atlases are not duplicated in this package because of
their size. Each is retrievable from CellxGene Discover at the exact version used here,
and the recorded digests allow a byte-level check after download.

## Reichart cardiomyopathy atlas (disease comparison, Figs. 4b, 4c, 5a and 5b)

- Reference: Reichart D, Lindberg EL, Maatz H, et al. Pathogenic variants damage cell
  composition and single cell transcription in cardiomyopathies. Science 2022;377:eabo1984.
  https://doi.org/10.1126/science.abo1984
- CellxGene collection: e75342a8-0f3b-4ec5-8ee1-245a23e0f7cb
- Dataset: "DCM/ACM heart cell atlas: All cells"
- Dataset ID: 65badd7a-9262-4fd1-9ce2-eb5dc0ca8039
- Dataset version ID: 9de5d490-b221-4529-875d-91d8b5c321e2
- Download URL: https://datasets.cellxgene.cziscience.com/9de5d490-b221-4529-875d-91d8b5c321e2.h5ad
- File name: reichart2022_dcm_acm_all.h5ad
- Size: 6,890,911,866 bytes (6.42 GiB), byte-exact against the CellxGene API
- SHA-256: 2815e0f14a8df840d95eb76aade9c62037a2b85e69fc35c36aafd110ab3afae5
- Contents: 881,081 nuclei, 32,383 genes, 79 donors, GRCh38
- Cells used here: the 284,771 nuclei annotated `cardiac muscle cell` whose donor
  carries `disease` of `dilated cardiomyopathy` (52 donors) or `normal` (18 donors)

`11_donor_pseudobulk_cardiomyocyte.py` consumes this file and writes the donor-level
table released as Online Resource 6. Raw counts are read from `raw/X`.

## Litvinukova adult-heart atlas (healthy localization, Fig. 4a)

- Reference: Litvinukova M, Talavera-Lopez C, Maatz H, et al. Cells of the adult human
  heart. Nature 2020;588:466-472. https://doi.org/10.1038/s41586-020-2797-4
- CellxGene collection: b52eb423-5d0d-4645-b217-e1c6d38b2e72
- Dataset version ID: a7f6822d-0e0e-451e-9858-af81392fcb9b (the identifier carried by the
  download URL below; the separate dataset ID was not recorded)
- Download URL: https://datasets.cellxgene.cziscience.com/a7f6822d-0e0e-451e-9858-af81392fcb9b.h5ad
- Size: 2,953,125,965 bytes (2.75 GiB), byte-exact against the CellxGene API
- SHA-256: not recorded. This atlas was used only for the healthy-heart localization
  panel and was not re-downloaded for the depth-sensitivity work, so no digest was
  taken at the time. The version-pinned URL above returns the exact file used; a
  digest can be computed on download but cannot be checked against a recorded value.
- Contents: 486,134 nuclei from 14 donors

The healthy cell-type summary derived from this atlas is released as Online
Resource 4, so the atlas itself is not required to reproduce Fig. 4a.

A copy of the Reichart atlas was retrieved from the URL above and verified against the recorded SHA-256 digest before the cross-cell-type depth-sensitivity analysis (`14_depth_sensitivity_crosscelltype.py`). The file itself is not included in this package because of its size; the digest above is sufficient to confirm that a freshly downloaded copy is the same one the analysis used.
