Retail tissue collection for mislabeling studies
Standardised collection of retail fish/seafood tissue (sushi, sashimi, fillets) for downstream species-ID. Captures the vendor's labelled species at purchase time as the a priori claim; preserved alongside the post-measurement call so mislabel audits always have both values visible. Upstream of species-ID assays such as COI barcoding.
Procedure Details
- Food-grade handling. Buy samples you or others would normally eat. Discard remaining tissue after excising the subsample if you don't intend to consume the rest.
- Labelling discipline in the field. Mislabeled tubes cascade into wrong BLAST calls downstream. Pre-print labels; cross-check tube → field log → LibreBiotech Sample ID before moving to the next vendor.
- Cold chain. On ice from purchase until freezer or extraction bench. Fresh at ambient acceptable for ≤ 4 h if extraction is same-day; otherwise −20 °C immediately.
- No cross-contamination. Fresh pick/scalpel per sample; change gloves between samples; no re-use of utensils.
Field kit (no reagents): smartphone/camera with EXIF timestamps; cooler bag with ≥ 2 h ice; 1.5–2 mL sample tubes (n + 20 % spares); sterile picks or disposable scalpels (one per sample); waterproof marker + pre-printed labels; field log (one row per sample).
Pre-printed labels are strongly recommended. Use a consistent scheme matching what will be registered in LibreBiotech, e.g. SashimiPilot-001, SashimiPilot-002, …
Target species list. Know in advance which taxa you're testing claims against — BLAST coverage against BOLD / NCBI nr is uneven across clades. Ward et al. 2005 is a solid reference for teleost fish.
Photograph the claim before the purchase. The vendor's label, menu entry, or signage showing the claimed species — with vendor name in frame.
- Per sample, ~3–5 minutes (longer at busy vendors if photography is constrained)
- Market trip total, 30–90 minutes depending on sample count
- Cold-chain budget: ≤ 4 h ambient before extraction or freezer; frozen indefinitely
Procedure Steps (Version 0.1.0)
Record the market trip metadata in your field log before any purchase: vendor / market name, location, date, session start time, collector.
Photograph the vendor's claim — label, menu entry, or display signage showing the claimed species with vendor name visible in frame.
Purchase the sample. Retain the receipt; photograph it separately.
Assign a unique Sample ID from your pre-printed label pool (e.g. SashimiPilot-001). Record it in the field log with vendor, claimed species as written, price, and purchase time.
Photograph the purchased piece with its Sample ID label visible — this is the physical provenance chain.
Excise ~20 mg tissue (rice-grain size) into the labelled tube using a fresh pick or scalpel. Close tightly.
Place tube in cooler with ice. Use a foam rack or zip bag to keep tubes off direct ice contact.
Change gloves; dispose of the used pick. No re-use across samples.
At session end, return to lab or home freezer. Register each Sample in LibreBiotech via create_samples_from_csv.py with the session's collection Process as process_id and the Sushi Truth Study attached via study_ids. Upload photos to a public store and capture the URL as annotation slot photo_ref on each Sample.
Per-sample deliverables at session end:
- Labelled tube in the cooler, ~20 mg excised tissue
- LibreBiotech Sample record pre-registered with
samples.organism_curie= NCBITaxon claim (as-labelled, not as-interpreted) and annotationscollected_at,vendor,purchase_price+unit_curie(currency),photo_refURL - Photos with EXIF timestamp preceding the Sample's
created_atin LibreBiotech — this is the audit story (claim preceded any measurement)
Record the claim as-labelled, not as-interpreted. Transliterate Japanese menu names, vernacular names, or vague labels verbatim. Do not guess the scientific species until post-BLAST — that defeats the claim-vs-measurement design.