Fish

Cultivated seafood — salmon, trout, and other teleosts — is an active cell-ag category pursued by companies including Wildtype, BlueNalu, and Umami Bioworks. This page collects the fixed data artifacts relevant to cultivated finfish: the Atlantic salmon genome-scale metabolic model, the AQUA-FAANG functional-annotation resource, and individual transcriptomic / proteomic deposits spanning muscle growth, myogenesis regulation, adipocyte differentiation, and storage/spoilage. “Fish” here spans the salmonids and other aquaculture teleosts surveyed for cultivated-meat work; it is a broad page covering many species rather than a single binomial.

Featured atlases

AQUA-FAANG

The FAANG consortium’s aquaculture programme — Advancing European Aquaculture by Genome Functional Annotation — generating genome-wide functional annotation maps for six aquaculture species important to European aquaculture (Atlantic salmon, rainbow trout, European sea bass, gilthead sea bream, common carp, turbot); the data hub hosts its open releases. A FAANG functional-annotation substrate for cell-ag-relevant aquaculture-cell-line work. Full entry in Databases.md / Livestock Multi-Tissue Atlases.

• AI Methods & Tooling
• Cell-line engineering
• Cell Lines & Engineering
• Single-cell atlases

Genome-scale metabolic models

GEMs are SBML-formatted reconstructions of an organism’s metabolic network — every reaction, every metabolite, every gene-protein-reaction mapping — and are the input data structure for the constraint-based modeling tools listed in Software.md / Metabolic Modeling & Strain Design. The salmon reconstruction below inherits network structure from the human reference GEMs catalogued in HumanReference.md.

SALARECON — Salmo salar (Atlantic salmon)

Whole-genome metabolic reconstruction of Atlantic salmon, published 2022 in PLOS Computational Biology, built to connect genome content to growth and feed-efficiency phenotypes for aquaculture. It is the most directly applicable existing GEM for cultivated salmonid modelling — though not purpose-built for cultivated meat — and relevant to the cultivated seafood category (salmon, trout) attracting investment from companies such as Umami Bioworks, BlueNalu, and Wildtype. SBML files distributed via the paper’s supplementary materials and the SALARECON repository at gitlab.com/digisal/salarecon.

Reference: Papers.md #84 (Zakhartsev et al. 2022, PLOS Computational Biology).

• AI Methods & Tooling
• Bioprocess & Scale-Up
• Bioreactor & scale-up
• Metabolic modeling
• Metabolism & Modeling

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Muscle growth & myogenesis

The bulk of the fish data surveyed here is skeletal-muscle transcriptomics across a wide taxonomic spread — the substrate for understanding how finfish muscle grows, the trait a cultivated-seafood process is built around. Studies span exercise-induced muscle remodelling in rainbow trout (SRA051669.1), myogenic regulatory genes in beltfish (SRX1674471), growth-hormone-transgenic coho salmon (PRJEB7712), spawning-associated muscle wasting in Atlantic cod (SRR955389–SRR955396), compensatory growth in fine flounder (SRS643409), age-series muscle transcriptomes in Schizothorax prenanti (SRP074282), microRNA–SmyD1 regulation in Chinese perch (GSE97173), fast- vs slow-growing phoenix barb (PRJNA848289), exercise-driven muscle-texture improvement in a hybrid cyprinid (PRJNA843454), pigmentation-linked muscular atrophy in Atlantic salmon (PRJNA706530), and a multi-population skeletal-muscle epigenomic study of large yellow croaker (Xie et al. 2024, Frontiers in Molecular Biosciences, PRJNA1124228) — the closest existing cultivated-yellow-croaker substrate.

Myoblast cell lines & myogenic differentiation

The most directly cultivated-meat-relevant fish datasets are the in-vitro ones. The establishment of a continuous myoblast cell line in the marine teleost Sebastes schlegelii (PRJNA661185, also CNGB CNP0000222) — propagated 50 passages over 150 days — and a proteomic characterisation of primary cultured gilthead sea bream myocytes across myogenic-differentiation stages together provide a close fish analogue to the bovine and porcine satellite-cell work that anchors cultivated-meat cell biology. A more recent label-free LC-MS/MS proteomic comparison of early (P3) vs late (P20) passages of an SBM Lates calcarifer muscle cell line (Pawaskar et al. 2026, Current Proteomics) profiles 454 proteins relevant to myogenic progression in barramundi — the dominant Indo-Pacific aquaculture finfish and an active cultivated-seafood target.

Adipocyte differentiation

Two microarray time-series profile finfish adipocyte biology — proliferation and differentiation of rainbow trout adipocyte precursor cells (GSE90058) and differentiation of the Atlantic salmon adipose-derived stromo-vascular fraction into adipocytes (GSE18389) — relevant to engineering the fat component of cultivated seafood.

Atlases, proteomes & quality profiling

A final cluster covers reference-scale and quality-oriented resources: a single-cell transcriptome atlas of zebrafish development (PRJNA564810), a spatial transcriptomic atlas of Atlantic salmon skin (PRJNA970983), the PeptideAtlas of the widely cultivated Labeo rohita (PRIDE PXD026377), a mass-spectrometry study of how fish-muscle metabolite profiles shift with sampling method, storage temperature, and time — directly relevant to cultivated-seafood quality and shelf-life — and a full-length-transcriptome / scRNA-seq atlas of Epinephelus coioides spleen (Huang et al. 2021, Frontiers in Immunology, SRP321375) which doubles as a methods reference for scRNA-seq pipeline development on aquaculture species without a reference genome. A single-nucleus immune atlas of the Atlantic salmon spleen (Sun et al. 2024, Fish & Shellfish Immunology; Roslin Institute) extends this reference-scale set into salmonids — 51,119 nuclei resolving nine major cell types, with an Aeromonas salmonicida challenge arm probing cell-specific infection responses — and pairs with the grouper-spleen atlas as a cross-species immune reference for cultivated-finfish work.

Complete data inventory

A curated snapshot spanning many finfish species. NCBI / EBI / Mendeley accessions are the canonical living source — fetch the linked accession for current sample counts, file sizes, and availability.

Study	Paper	Data	Type	Species	Tissue	Description	Size	Area of research
A single-cell transcriptome atlas for zebrafish development	DOI	PRJNA564810	scRNA-seq	Danio rerio	Whole embryo	Whole zebrafish embryos at 1/2/5 dpf, 220 cell types, n=2 per timepoint	44,102 cells, 525 Gb	Cell-type atlas
Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish	DOI	SRA051669.1	RNA-seq	Oncorhynchus mykiss	Muscle	Red/white muscle of rainbow trout rested (n=10) or swum 1176 km over 40 days (n=10)	3.4 Gb	Muscle growth
Identification of myogenic regulatory genes in the muscle transcriptome of beltfish	DOI	SRX1674471	RNA-seq	Trichiurus lepturus	Muscle	Muscle tissue of a wild juvenile beltfish (n=1)	15.8 Gb	Myogenesis regulation
RNA-seq of fast skeletal muscle in restriction-fed transgenic coho salmon	DOI	PRJEB7712	RNA-seq	Oncorhynchus kisutch	Muscle	Fast skeletal muscle, GH-transgenic (n=6) and wildtype (n=6) coho salmon	132 Gb	Muscle growth regulation
Transcriptomic landscape of Atlantic salmon skin	DOI	PRJNA970983	RNA-seq (spatial)	Salmo salar	Skin	Skin tissue from 4 body locations in 2 Atlantic salmon	78.6 Gb	Spatial transcriptomic atlas
Proteomic characterization of primary cultured myocytes in a fish model at different myogenesis stages	DOI	supplementary	LC-MS/MS	Sparus aurata	Muscle	Primary satellite cells at 4/8/12 days culture (n=5 each); 2-D gel + LC-MS/MS; data in the paper’s supplementary file	898 spots	Myogenesis
Substantial downregulation of myogenic transcripts in skeletal muscle of Atlantic cod during the spawning period	DOI	SRR955389	RNA-seq	Gadus morhua	Muscle	Skeletal muscle from 3 sampling time points, 6 male + 6 female fish (runs SRR955389–SRR955396)	—	Muscle wasting
Establishment of a myoblast cell line in the marine teleost Sebastes schlegelii	DOI	PRJNA661185	RNA-seq	Sebastes schlegelii	Muscle	Continuous myoblast cell line, explant method, 50 passages over 150 days (also CNGB CNP0000222)	105.2 Gb	Muscle cell line
RNA-seq analysis of compensatory growth in the skeletal muscle of fine flounder	DOI	SRS643409	RNA-seq	Paralichthys adspersus	Muscle	Feeding-regime and fasting groups, weeks 0/3/4	3 Gb	Muscle growth
Gene expression during proliferation and differentiation of rainbow trout adipocyte precursor cells	DOI	GSE90058	Microarray	Oncorhynchus mykiss	Fat	Timepoints at days 3/8/15/21	52.5 Mb	Adipocyte proliferation & differentiation
Gene expression in Atlantic salmon adipose-derived stromo-vascular fraction during adipocyte differentiation	DOI	GSE18389	Microarray	Salmo salar	Fat	6 time-points across adipocyte differentiation	6.1 Mb	Adipocyte differentiation
Characterization of the muscle transcriptome in Schizothorax prenanti	DOI	SRP074282	RNA-seq	Schizothorax prenanti	Muscle	Skeletal muscle at 3 time points: 30-day larva, 1 year, 3 years	19.7 Gb	Muscle growth regulation
Proteomic and microRNA transcriptome analysis of the microRNA-SmyD1 network in Chinese perch skeletal muscle	DOI	GSE97173	Microarray	Siniperca chuatsi	Muscle	Red and white muscle from 2-year-old Chinese perch	~3 Mb	Muscle protein expression
Transcriptome analysis of the muscle of fast- and slow-growing phoenix barb	DOI	PRJNA848289	RNA-seq	Spinibarbus denticulatus denticulatus	Muscle	Muscle at 3 growth stages; liver, muscle, brain also collected; 10 individuals	153 Gb	Muscle growth
Comparative transcriptome analysis of muscle textural quality improvement by exercise in a hybrid cyprinid	DOI	PRJNA843454	RNA-seq	Erythroculter ilishaeformis × Ancherythroculter nigrocauda	Muscle	Hybrid cyprinid; 12 samples (covers both parent species)	76 Gb	Muscle texture
Metabolic profile of fish muscle tissue changes with sampling method, storage strategy and time	DOI	Mendeley	Mass spectrometry peak list	Oncorhynchus mykiss	Muscle	45 samples, 6 timepoints, 3 storage temperatures, 4 sampling/storage methods	4.08 Mb	Storage
The PeptideAtlas of the widely cultivated fish Labeo rohita	DOI	PXD026377	Mass spectrometry (DDA-MS/MS)	Labeo rohita	Multiple	Multi-tissue peptide atlas	295 raw files	Protein atlas
Histological and transcriptomic analysis of muscular atrophy linked to depleted flesh pigmentation in Atlantic salmon	DOI	PRJNA706530	RNA-seq	Salmo salar	Muscle	15 fish (3 flesh-colour groups, n=5), two muscle regions	348 Gb	Muscle pigmentation & integrity
Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome	DOI	SRP321375	scRNA-seq + full-length transcriptome (PacBio)	Epinephelus coioides	Spleen	scRNA-seq of orange-spotted grouper spleen following Pseudomonas plecoglossicida infection; full-length transcriptome reconstruction without reference genome; doubles as a methods reference for aquaculture species lacking a reference genome; reuses related-species reference PRJNA625542	—	Immune-cell atlas & scRNA-seq methodology
Skeletal muscle feature of different populations in large yellow croaker (Larimichthys crocea): from an epigenetic point of view	DOI	PRJNA1124228	WGBS (BS-seq)	Larimichthys crocea	Muscle	Whole-genome bisulfite sequencing of skeletal muscle across five large yellow croaker populations (ZS, JM, ZJ, XS, ND); 42 pooled samples; methylation-profile comparison	—	Population epigenomics & muscle quality
Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection	DOI	GSE252828	snRNA-seq (single-nucleus)	Salmo salar	Spleen	Single-nucleus immune atlas of the Atlantic salmon spleen (Sun et al. 2024, Fish & Shellfish Immunology; Roslin Institute); 51,119 nuclei resolving nine major cell types, with an Aeromonas salmonicida bacterial-challenge arm probing cell-specific infection responses	—	Immune-cell atlas
Proteomic insights into myogenic progression in cultured muscle cells of Lates calcarifer (Bloch, 1790)	DOI	supplementary	Label-free LC-MS/MS proteomics	Lates calcarifer	Muscle	Comparative proteomics of early (P3) vs late (P20) passages of an SBM Lates calcarifer muscle cell line; 454 proteins identified; no public proteomics deposit — supplementary file only	—	Aquaculture cultured-muscle proteomics
Establishment of spontaneously immortalized Japanese eel muscle-derived preadipocyte cell lines for cultured seafood production	DOI	supplementary	Immortalized cell lines	Anguilla japonica	Muscle (preadipocyte)	Three spontaneously immortalized muscle-derived preadipocyte lines (JE-KRT224, JE-EK9, JE-F1140), >120 population doublings, lipid accumulation with fatty-acid profiles matching native eel meat; lines deposited at NITE (BP-04244/BP-04246/BP-04247); characterization data in supplementary	3 cell lines	Adipocyte cell lines for cultivated seafood
Establishment and characterization of continuous satellite muscle cells from olive flounder (Paralichthys olivaceus)	DOI	on request	Immortalized cell line	Paralichthys olivaceus	Muscle (satellite cells)	Continuous satellite-cell line (OF20IMC) spontaneously immortalized by passage 20; myotube differentiation with MyoD, myogenin and desmin expression; data from the corresponding author on request	—	Muscle cell line & myogenesis
Development of serum-reduced medium for mackerel muscle cell line cultivation	DOI	supplementary	Cell growth assays	Scomber scombrus	Muscle (myoblast)	Serum-reduced medium development for the Atlantic mackerel Mack1 muscle cell line; screened non-animal protein isolates (rapeseed, chlorella, spirulina) and defined additives; F-12 plus rapeseed isolate supported >30 doublings over 55 days; growth-assay data in supporting information	—	Media optimization (serum reduction)
Genome-scale metabolic network reconstruction of model animals as a platform for translational research	DOI	Zebrafish-GEM	Genome-scale metabolic model (SBML)	Danio rerio	Whole organism	Curated zebrafish GEM derived from Human-GEM; 12,910 reactions, 8,347 metabolites, 2,714 genes; SBML and MATLAB files; released alongside mouse, rat, fruit-fly and worm reconstructions; v1.6.0	12,910 reactions, 2,714 genes	Metabolic modeling
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development (Daniocell)	DOI	GSE223922	scRNA-seq	Danio rerio	Whole embryo / larva	Whole-animal wild-type zebrafish across 62 stages (3-120 hpf), 489,686 cells, MULTI-seq cell hashing; browsable via the Daniocell portal	489,686 cells	Developmental cell-type atlas
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors (Zebrahub)	DOI	PRJNA940501	scRNA-seq (single-embryo)	Danio rerio	Whole embryo / larva	Single-embryo scRNA-seq atlas across 10 stages (bud to 10 dpf), ~120,671 cells, paired with light-sheet lineage reconstructions; processed atlas on figshare (record 20510367) and the Zebrahub portal	~120,671 cells	Developmental cell-type atlas
Single-cell atlas in the living fossil Yangtze sturgeon provides insight into the evolution of fish	DOI	PRJNA1121101	scRNA-seq + Iso-seq	Acipenser dabryanus	Multiple (17 tissues)	Body-wide single-cell atlas across 17 tissues, 82,401 cells; paired full-length transcriptome (SRA PRJNA1121939); cross-species comparison against nurse shark and zebrafish	82,401 cells	Whole-body cell-type atlas
Distinct muscle stem cell fates correlated with hyperplasia and hypertrophy during skeletal muscle growth in rainbow trout	preprint	none named	scRNA-seq	Oncorhynchus mykiss	Muscle	Single-cell atlas of muscle-derived cells across five growth stages; 15 resident populations including eight myogenic subtypes; RNA-velocity reveals distinct hyperplasia vs hypertrophy trajectories and a pax7+/pdgfrα+ subpopulation; bioRxiv preprint	—	Muscle stem-cell biology
Characterization of myogenesis in European sea bass (Dicentrarchus labrax) using primary white muscle cell cultures	DOI	supplementary	Primary cell culture (qPCR/IF)	Dicentrarchus labrax	Muscle (white)	In-vitro myogenesis in primary white muscle cells over a 12-day culture; myogenic-marker expression by qPCR and immunofluorescence; no sequencing deposited, data in article and supplementary	—	Myogenesis
Continuous fish muscle cell line with capacity for myogenic and adipogenic-like phenotypes	DOI	OSF	Untargeted lipidomics (HR-LC-MS/MS)	Scomber scombrus	Muscle (immortalized cell line)	MACK1, a spontaneously immortalized Atlantic mackerel skeletal-muscle cell line with both myogenic and adipogenic-like differentiation capacity, developed as a cultivated-seafood substrate (Saad et al. 2023, Scientific Reports); the OSF deposit holds untargeted lipidomics (HR-LC-MS/MS, n=3) of adipogenic-like cells after 14-day lipid accumulation	n=3	Muscle/fat cell line

Curation source: The deposit entries above were initially curated from the supplemental Table 1 of Todhunter et al. 2024 (Papers.md ref #132). Subsequent additions come from CAAIL contributors.

Further reading

• Adjacent research areas: Cellular Engineering, Media Optimization, Bioprocess Control, Sensory Prediction (hyperspectral off-flavor profiling in cultured salmonids), Metabolic Modeling.
• Atlases & functional genomics: Livestock Multi-Tissue Atlases & Functional Genomics in Databases.md.
• Seafood species references: PISCES and ATLAS in Databases.md.
• Sequence & expression repositories: GEO, SRA, Ensembl, GenBank — the canonical living indexes for the deposits curated here.
• Cross-species modeling tooling: TranscriptFormer and UCE in Software.md.
• Adjacent single-cell atlases: Farnsworth et al. 2020, Developmental Biology, A single-cell transcriptome atlas for zebrafish development — developmental scRNA atlas in zebrafish, an obligate cross-species reference for cultivated-finfish single-cell work given the lack of comparable resources in aquaculture species.
• Reference substrates: HumanReference, CHOReference, CrossSpecies. AI/ML benchmarks: Benchmarks.