Mollusk

Cultivated mollusk meat — mussels, scallops, oysters, and snails — is an early-stage cell-ag category. This page collects the fixed data artifacts relevant to cultivating mollusk cells: transcriptomic and proteomic deposits spanning muscle tissue analysis, adductor-muscle differentiation, toxin response, and molecular-resource development across bivalves and gastropods. No GTEx-style atlas or genome-scale metabolic model exists for any mollusk yet; the data here is individual study deposits.

Muscle tissue transcriptomics & differentiation

The mollusk muscle datasets are predominantly comparative transcriptomics across tissues and muscle types. RNA-seq of mantle, muscle, and gill in the Mediterranean mussel (SRP033481) and of foot muscle versus mantle in the giant triton snail (PRJNA695322) characterise tissue-specific expression, while a fast- vs slow-muscle proteomic/transcriptomic study in the Yesso scallop and a microRNA signature of its striated versus smooth adductor muscles (PRJNA822005) probe muscle-type differentiation — relevant background for any cultivated-mollusk muscle-tissue work. A single-cell RNA-seq atlas of the same scallop’s adductor muscle (Sun et al. 2021, Genomics) resolves 20 cell clusters across four broad classes — mesenchymal stem cells, muscle cells, neurons, and haemolymph cells — with pseudotemporal differentiation trajectories, the closest cell-type reference for cultivated-mollusk muscle tissue engineering.

Toxin response & molecular-resource development

Two further datasets sit outside the muscle focus: an RNA-seq profile of the queen scallop digestive gland after exposure to domoic-acid-producing algae (PRJNA508885), relevant to contamination and food-safety screening; and an early RNA-seq-based molecular-resource effort for the freshwater mussel Villosa lienosa (SRP009061), a reference-building dataset for a species with little prior sequence data.

Single-cell atlases

Whole-organ single-cell atlases of bivalves have begun to appear. A scRNA-seq cell atlas of the Hong Kong oyster (Crassostrea hongkongensis) gill (Ma & Wang 2025, Environmental Science & Technology) identifies 18 cell types — including newly described copper-accumulating “copperphilic” cells — and an early-development scRNA-seq study of the Pacific oyster Crassostrea (Magallana) gigas (Gavery et al. 2025, BMC Genomics) maps primordial-germ-cell specification and early developmental cell states across cleavage, blastula, and gastrula stages. Both are early but useful cell-type and developmental references for cultivated-mollusk work that needs to identify and track the cell populations a bivalve culture would propagate.

Complete data inventory

A curated snapshot. NCBI / ProteomeXchange 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
RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics among different tissues	DOI	SRP033481	RNA-seq	Mytilus galloprovincialis	Mantle, Muscle, Gill	Mantle, muscle, and gill from 5 mussels; 2 biological replicates per tissue (gill: 1)	33.7 Gb	Muscle tissue analysis
Novel copper-responsive cell subtypes in oyster gills: scRNA-seq uncovers detoxification strategy and intraspecific accumulation variation	DOI	PRJNA1467315	scRNA-seq	Crassostrea hongkongensis (syn. Magallana hongkongensis)	Gill	First cell atlas of oyster gills at single-cell resolution (Ma & Wang 2025, Environmental Science & Technology); 18 cell types, including newly identified copper-accumulating copperphilic cells, with cell-differentiation trajectories and cell-type-specific stress / ion-transport pathways	—	Single-cell atlas
Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq	DOI	none named	scRNA-seq	Patinopecten yessoensis	Muscle (adductor)	scRNA-seq atlas of scallop adductor muscle (Sun et al. 2021, Genomics); 20 cell clusters across four broad classes — mesenchymal stem cells, muscle cells, neurons, and haemolymph cells — with pseudotemporal differentiation trajectories; neurons resolved in striated but not smooth adductor muscle; the paper names no data deposit	—	Single-cell atlas & muscle differentiation
Primordial germ cell specification and early developmental cell states in Pacific oyster	DOI	PRJNA906172	scRNA-seq	Crassostrea (Magallana) gigas	Whole embryo (cleavage–gastrula)	Early-development scRNA-seq of the Pacific oyster (Gavery et al. 2025, BMC Genomics); maps primordial-germ-cell specification and early developmental cell states across cleavage, blastula, and gastrula stages	—	Single-cell atlas (development)
Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics	DOI	PXD005166	RNA-seq, mass spectrometry	Patinopecten yessoensis	Muscle	Transcriptomic and proteomic, 2 biological replicates, 6 individuals; SRA run SRR4254476 marked unavailable in source	~94 M reads	Muscle tissue analysis
Rapid development of molecular resources for the freshwater mussel Villosa lienosa	DOI	SRP009061	RNA-seq, contigs	Villosa lienosa	Mantle, Muscle, Gill	RNA-seq of 4 samples; also GenBank contigs JR494687–JR540729	16.2 Gb	Molecular-resource development
RNA-Seq transcriptome profiling of the queen scallop digestive gland after domoic-acid exposure	DOI	PRJNA508885	RNA-seq	Aequipecten opercularis	Digestive gland	Digestive-gland transcriptome after exposure to domoic-acid-producing Pseudo-nitzschia	~968 M filtered reads	Toxin response
Comparative transcriptomic profiles between foot muscle and mantle in the giant triton snail	DOI	PRJNA695322	RNA-seq	Charonia tritonis	Muscle, Mantle	Foot muscle and mantle tissue from adult C. tritonis	7 Gb	Muscle tissue analysis
MicroRNA expression signature in the striated and smooth adductor muscles of the Yesso scallop	DOI	PRJNA822005	miRNA-seq	Patinopecten yessoensis	Muscle	Striated and smooth adductor-muscle tissue from young adults	4 Gb	Muscle growth & differentiation
Oyster cellular architecture and innate immune programs resolved by single-cell RNA sequencing	DOI	PRJNA1381342	scRNA-seq	Crassostrea hongkongensis (syn. Magallana hongkongensis)	Gill	Tissue-resolved single-cell gill atlas of the Hong Kong oyster (Chen & Wang 2026, Fish & Shellfish Immunology); 20 cell types, including a diversified five-member phagocyte lineage with distinct extracellular-containment, intracellular-clearance, and matrix-restoration strategies, plus three humoral immune populations and a neural-related compartment	—	Single-cell atlas & immunity
Single-cell transcriptomic dynamics of scallop heart reveals the heterogeneous response to heat stress	DOI	PRJNA1187280	scRNA-seq	Argopecten irradians	Heart	scRNA-seq of bay-scallop heart under graded heat stress (Wang et al. 2025, BMC Biology); 50,048 cells across normal, maximum, and heart-rate-drop groups; two cardiomyocyte subpopulations (ventricular and atrial myocytes) with distinct thermal-stress roles, and PLRP2-like identified as the top heat-responsive gene by RNAi	—	Single-cell atlas & stress response
Diversity and functional specialization of oyster immune cells uncovered by integrative single-cell level investigations	DOI	PRJEB74031	scRNA-seq	Crassostrea (Magallana) gigas	Hemocytes	Integrative single-cell characterization of Pacific-oyster hemocytes (De La Forest Divonne et al. 2025, eLife); at least seven functionally distinct immune-cell types and three hematopoietic lineages resolved by combining scRNA-seq with cytology, cell sorting, and functional assays; ties molecular clusters to phagocytosis, ROS production, copper accumulation, and antimicrobial-peptide expression	—	Single-cell atlas & immunity
Integrative analysis of single-nucleus RNA-seq and bulk RNA-seq reveals germline cells development dynamics and niches in the Pacific oyster gonad	DOI	PRJNA983861	snRNA-seq, RNA-seq	Crassostrea (Magallana) gigas	Gonad	snRNA-seq of Pacific-oyster gonad integrated with bulk RNA-seq (Wang et al. 2024, iScience); 13,683 nuclei (6,452 male, 7,231 female) resolving 23 male and 19 female clusters, with follicular cells in females and Sertoli/Leydig-like cells in males; NOTCH and BMP signaling mark the male germline niche; integrates reused public bulk gonad RNA-seq (SRA SRP112367)	—	Single-cell atlas & germline niche
Metabolic reprogramming and mitochondrial dysfunction underlie β gonia arrest and niche cell dysfunction in sterile triploid oysters	DOI	PRJNA1244049	Spatial transcriptomics, snRNA-seq	Crassostrea (Magallana) gigas	Gonad	Spatially resolved molecular atlas of sterile triploid oyster gonad integrating Stereo-seq spatial transcriptomics with snRNA-seq (Wang et al. 2025, Communications Biology); 9,356 triploid and 11,286 diploid nuclei plus a triploid-female gonad tissue section; characterizes β-gonia transcriptional dysregulation, impaired ATP synthesis, and disrupted niche-cell interactions underlying partial triploid sterility	—	Single-cell atlas & germline niche

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, Bioprocess Control, Media Optimization.
• Sequence & expression repositories: GEO, SRA, Ensembl — the canonical living indexes for the deposits curated here.
• Alternative-seafood species references: Seafood Species Reference Databases in Databases.md.
• Cross-species modeling tooling: TranscriptFormer and UCE in Software.md — relevant where labelled mollusk data is sparse.
• Reference substrates: HumanReference, CHOReference, CrossSpecies. AI/ML benchmarks: Benchmarks.