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Paired canine mammary-stroma RNA and protein

canine-mammary-stroma imports the processed measurements of Amini et al. (2021), GSE135183 and PXD023023. It uses the same data commands and QuantitativeDataset API as other species and sources:

orfdata data info canine-mammary-stroma
orfdata data fetch canine-mammary-stroma
orfdata data path canine-mammary-stroma

from orfdata import DatasetRegistry

registry = DatasetRegistry()
dataset = registry.open("canine-mammary-stroma")  # Offline; no implicit download.
rna_reference, protein_reference = dataset.manifest.references
pairs = list(dataset.pairings())
complete_pairs = [pair for pair in pairs if pair.right_assay_id is not None]
pair = complete_pairs[0]
rna = dataset.measurements(
    reference=pair.reference, assay_id=pair.left_assay_id, unit="estimated_count"
)
protein = dataset.measurements(
    reference=pair.right_reference, assay_id=pair.right_assay_id, unit="LFQ intensity"
)

The release contains 993,560 native measurements in a 52 MB download and a 514 MB installed SQLite file. Rebuilding uses approximately 8 MB of pinned processed inputs; no raw MS files, sequencing reads, alignment index or vendor database is required.

Layer Native scope Quantities
RNA 18,582 Ensembl gene IDs × 30 samples, 15 cases Integer estimated counts from Kallisto/tximport
Protein 1,583 native MaxQuant groups × 28 samples, 14 cases Intensity, LFQ intensity, iBAQ
Peptide 5,413 native peptide rows × 28 samples Intensity and the separately reported LFQ intensity columns

Different quantitative columns do not add biological replicates. The 58 assays retain their original sample and run identities. Native MS rows include 77 reversed protein groups and 52 contaminant groups; these counts are not counts of confidently detected canine proteins.

Specimen pairing

The authors reused archived FFPE mammary specimens for separate laser-capture RNA and protein preparations. The importer verifies a unique match between clinical Table 1 and GEO by breed, age and histological subtype, recording spelling normalizations and both original sets of labels. This is a metadata-derived crosswalk within an author-declared shared cohort, not an author-provided case-ID mapping.

Fourteen shared cases give 28 complete assay pairs: normal stroma and cancer-associated stroma separately. Two RNA samples from GEO case 127 have explicitly missing protein mates; the paper reports exclusion of proteomics case 7 because its paraffin block was unavailable. No protein sample is invented.

These pairs use same_specimen. This basis means separate preparations from the same original specimen, without claiming identical aliquots or adjacent sections. Temporal labels refer to the original biological specimen, not the dates of RNA sequencing and mass-spectrometry acquisition. Missing mates retain an unknown temporal relationship. Pairing does not itself establish a relationship between RNA genes and protein groups: this release has no cross-modal target relations or current-reference mappings.

The normal compartment belongs to a cancer-bearing mammary specimen. It is not a healthy-animal normal-tissue atlas. Source case IDs identify individual specimens, and repeated compartments or quantities never imply additional dogs.

Missingness, native records and reference limits

  • RNA zeros remain measured zero counts. Counts are estimated gene-level values, with no conversion to TPM, copies per cell or translation efficiency.
  • MaxQuant MS zeros denote unquantified cells. Their numeric values are None with status missing; the original "0" survives in provenance. The 2,156 native "NaN" iBAQ cells also remain missing, with a separate reason.
  • Every native MS field survives once in the corresponding mapping's provenance["native_record"]. Measurements retain source row/column, original numeric text, identification type and the original control/decoy flags.
  • Peptide mappings retain every reported native protein-group ID. A unique assignment to one group is not unique protein or isoform detection. Group records retain reported protein labels, including contaminants, without assigning them to a canine biological protein reference.
  • No source QC threshold, aggregation, imputation, differential-expression model or RNA/protein ratio is applied. Consumers can inspect the native flags and scores explicitly.

RNA was quantified against Ensembl transcripts on CanFam3.1; its exact release and transcript sequence bytes are not reported. The protein search used a canonical UniProt dog reference dated 2019-07-29 with decoys and contaminants; the searched FASTA is absent from the deposited processed files. Both references remain source-bound and incomplete. Source membership and uniqueness flags are preserved, but no full-background sequence uniqueness is asserted. These data provide neither ncORF translation evidence nor MHC-presentation evidence.

The earlier source audit records the acquisition and crosswalk evidence. The PRIDE project declares CC0; GEO numerical data and factual metadata use GEO's public-data terms. Factual clinical curation cites Table 1 of the CC BY-NC-ND article. Its original text and figures are excluded from the dataset artifact.