Canine paired measurements and translation-evidence audit¶
Source check: 28 October 2026. This audit identifies importable measurement files and their limitations. The subsequent mammary-stroma importer now exposes the paired study through the common quantitative registry. The machine-readable audit contains source URLs, hashes, counts, search queries and a candidate sample crosswalk.
Paired RNA and protein: a verified study¶
Amini et al., 2021 studied cancer-associated and normal stroma from archived canine mammary carcinomas. The authors explicitly reused the cases of their earlier RNA study. Original case 7 was excluded from proteomics because its paraffin block was unavailable. Measurements come from separate laser-capture preparations of the same tissue cases, not identical RNA/protein aliquots.
| Source | Verified processed data | Download |
|---|---|---|
| GSE135183 | 18,582 genes × 30 RNA samples, 15 cases with two stromal compartments | Raw counts, 606 KB compressed |
| PXD023023 | 1,583 native protein-group rows with 28 LFQ sample columns | Protein groups, 2.8 MB |
| PXD023023 | 5,413 peptide rows with native quantitative fields | Peptides, 4.5 MB |
The downloaded protein and peptide files match PRIDE's deposited SHA-1 checksums; the audit also records SHA-256 for all three processed files. RNA values are nonnegative integer counts. Native protein-group counts include controls and contaminants and are not counts of confidently detected biological proteins.
PRIDE filenames use case numbers 1–15; GEO uses case IDs such as 109 and 135. Matching the article's Table 1 to GEO by breed, age and histological subtype uniquely reconciles all 14 proteomics cases. The resulting 28 sample links are metadata-derived, not an author-supplied identifier crosswalk. Breed spelling normalizations are recorded. GEO case 127 is the unmatched RNA case.
An importer must retain that pairing basis, separate stromal compartments,
protein-group ambiguity, controls, missing quantities and native units. The
deposited search used a dated canonical UniProt reference, but its FASTA is not
among the 31 PRIDE files. Sequence/reference qualification remains necessary;
these data do not establish ncORF translation. Author-derived contrasts in the
supplementary workbooks must stay distinct from sample-level measurements.
The paired study is now imported as canine-mammary-stroma; the remaining dog
data requests stay tracked in #20.
Dog Ribo-seq and ncORF translation¶
The date-stamped dog-specific SRA, GEO and ENA queries in the audit returned no matching sequencing records. This is a bounded repository search, not proof that no unpublished or differently indexed experiment exists.
Pfeffer et al., 2015 reports ribosome profiling and total RNA sequencing of canine pancreas rough-ER preparations aligned to CanFam3.1/Ensembl 77. Its accession section lists EMDB and PDB deposits, without a sequencing accession. No downloadable reads or processed ORF-level counts were verified in this audit. Even if recovered, the preparation would describe an enriched pancreatic compartment, not a broad normal-tissue canine translatome.
Existing canine PeptideAtlas, Pfizer and DLA datasets retain their deposited canonical-search scope. The experimental dog ncORF search pipeline is a route to new analysis, not a released experimentally supported catalogue. Dog ncORF translation coverage therefore remains unavailable pending qualified data or a separately validated reanalysis. See #12.