Crustacean

Cultivated crustacean meat — primarily shrimp — is a growing cell-ag category. This page collects the fixed data artifacts relevant to cultivating crustacean cells: transcriptomic deposits spanning muscle growth, feed efficiency, molting, embryogenesis, and stress response, predominantly in the Pacific white shrimp Litopenaeus vannamei with additional coverage of crab, prawn, and crayfish. No GTEx-style atlas or genome-scale metabolic model exists for any crustacean yet; the data here is individual study deposits.

Muscle growth & growth performance

The largest cluster of crustacean data profiles muscle transcriptomes against growth rate and feed efficiency — the economically central traits, and the proxy for the muscle-yield questions a cultivated-crustacean process would face. Studies compare fast- vs slow-growing Pacific white shrimp (PRJNA987844, SRP128934), the molecular basis of residual feed intake (SRR5134062/SRR5135715), rapid- vs slow-growing Penaeus vannamei across multiple tissues (BioProject uid 11915669), growth-trait genes in kuruma shrimp (SRP304278), and claw-muscle transcriptomes of mud crab across fattening stages (PRJNA389966).

Molting, metamorphosis & embryogenesis

Crustacean muscle is remodelled across the molt cycle and through metamorphosis — a developmental complexity with no direct livestock parallel. Datasets cover early development of Pacific white shrimp from zygote to postlarvae (SRR1460493–SRR1460505), whole-transcriptome molting analysis across inter-, pre-, and post-molt stages (SRX1098368–SRX1098375), microRNA profiling of claw muscle across molt stages in the Chinese mitten crab (SRR7990528–SRR7990530), and late embryogenesis of the red claw crayfish (PRJNA577772).

Stress response

Two datasets profile the muscle transcriptomic response to environmental stress — low-temperature stress in Pacific white shrimp (SRP095377) and chronic hypoxia across hepatopancreas, muscle, and gill in the oriental river prawn (SRP056408) — relevant to bioprocess-condition tolerance.

Regeneration & muscle-system biology

The Chinese mitten crab limb-regeneration multi-omics dataset (PRJNA737102 and companion BioProjects, plus NGDC CRA003690) is a rare regeneration resource with a genome assembly and a limb-regeneration RNA-seq time-course. A study of actin genes and their expression in Pacific white shrimp is also catalogued, though the source survey links it only to journal articles rather than a repository accession.

Single-cell atlases

Cell-type-resolved atlases of cultivation-relevant crustaceans have begun to appear, concentrated in the hepatopancreas and hemocytes of Pacific white shrimp and giant freshwater prawn. Three single-cell / single-nucleus atlases resolve the Litopenaeus vannamei hepatopancreas — epithelial cell types plus supporting cells, profiled under Vibrio and AHPND challenge — and a fourth maps giant freshwater prawn (Macrobrachium rosenbergii) hemocytes with differentiation trajectories and viral tropism. They are early cell-type label sources for the dominant cultivated-shrimp species, useful for cross-species transfer and for characterising the cell populations a cultivated-crustacean process would propagate.

Complete data inventory

A curated snapshot. NCBI / NGDC 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 sequencing and lncRNA identification in muscle of the Pacific white shrimp at different growth rates	DOI	`PRJNA987844`	RNA-seq	Litopenaeus vannamei	Muscle	22 fast-growing + 22 slow-growing shrimp, 4 months of age	289 Gb	Muscle growth
Single-cell transcriptomic atlas of shrimp hepatopancreas reveals an endoplasmic reticulum stress-dependent immune response to Vibrio parahaemolyticus infection	DOI	on request	snRNA-seq	Litopenaeus vannamei	Hepatopancreas	Single-nucleus atlas of Pacific white shrimp hepatopancreas (Lu et al. 2026, Fish & Shellfish Immunology); 20,000+ cells classified into five cell types (B, F, E, M, and R cells); endoplasmic-reticulum-stress and cell-death pathways under Vibrio parahaemolyticus; the authors state the data are available on request (no public deposit)	—	Single-cell atlas
Single-cell transcriptomics of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas reveal immune and metabolic responses to AHPND-causing Vibrio parahaemolyticus	DOI	`GSE306674`	scRNA-seq	Litopenaeus vannamei	Hepatopancreas	Healthy and AHPND-infected hepatopancreas (Aldersey et al. 2026, Frontiers in Immunology); 27,374 integrated cells across nine clusters including epithelial, myocyte, and hemocyte populations; oxidative-stress and energy-metabolism reprogramming	—	Single-cell atlas
Generation of a Litopenaeus vannamei hepatopancreas cell atlas from single nuclei transcriptomics using a new nuclei isolation method	DOI	`PRJNA1302321`	snRNA-seq	Litopenaeus vannamei	Hepatopancreas	Hepatopancreas cell atlas (Florea et al. 2025, BMC Genomics); 4,005 cells across nine clusters; introduces a TST-based crustacean nuclei-isolation protocol; hepatocyte subtypes plus fibroblasts, myocytes, and intestinal epithelial cells	—	Single-cell atlas
Single-cell RNA sequencing reveals hemocyte heterogeneity, differentiation trajectories, and viral tropism in shrimp (Macrobrachium rosenbergii) infected with decapodiridovirus litopenaeus1	DOI	`CRA022393`	scRNA-seq	Macrobrachium rosenbergii	Hemocytes	First single-cell atlas of giant freshwater prawn hemocytes under decapodiridovirus (DIV1) infection (Xiao et al. 2025, Journal of Virology); 12 clusters with pseudotime differentiation trajectories and cell-type-specific viral tropism	—	Single-cell atlas
Comparative transcriptome analysis of Pacific white shrimp muscle and residual feed intake	DOI	`SRR5134062`	RNA-seq	Litopenaeus vannamei	Muscle	Third-abdominal-segment muscle, 33 families of 12 individuals (also `SRR5135715`)	85.1 Gb	Feed efficiency
Transcriptome analysis of activated genes in Litopenaeus vannamei families of superior growth performance	DOI	`SRP128934`	RNA-seq	Litopenaeus vannamei	Muscle	Muscle tissue from pleopods	~320 Gb	Weight growth
Comparative transcriptomic characterization of early development in Pacific white shrimp	DOI	`SRR1460493`	RNA-seq	Litopenaeus vannamei	Muscle, Exoskeleton	15 samples per developmental stage from zygote to postlarvae (runs `SRR1460493`–`SRR1460505`)	12 Gb	Metamorphosis
Whole transcriptome analysis of molecular mechanisms for molting in Litopenaeus vannamei	DOI	`SRX1098368`	RNA-seq	Litopenaeus vannamei	Muscle, Exoskeleton	Inter-molt, pre-molt, and post-molt stages (runs `SRX1098368`–`SRX1098375`)	13 Gb	Molting
Actin genes and their expression in Pacific white shrimp	DOI	unavailable	RNA-seq	Litopenaeus vannamei	Muscle, Exoskeleton	Source survey links only journal articles (doi:10.1371/journal.pone.0106201, doi:10.1371/journal.pone.0144350), no repository accession	—	Muscle-system biology
Transcriptome difference between rapid-growing and slow-growing Penaeus vannamei	DOI	`PRJNA664224`	RNA-seq	Penaeus vannamei	Eyestalk, Hepatopancreas, Intestinal tract	Eyestalk, hepatopancreas, and intestinal-tract tissue from 6 samples	49 Gb	Growth
Growth-trait gene analysis of kuruma shrimp by transcriptome study	DOI	`SRP304278`	RNA-seq	Marsupenaeus japonicus	Muscle	Fast-growth and slow-growth groups	90.4 Gb	Growth
Transcriptome profiling of claw muscle of the mud crab at different fattening stages	DOI	`PRJNA389966`	RNA-seq	Scylla paramamosain	Muscle	Samples from three fattening stages (B, C, D)	39 Gb	Muscle growth
Identification of Eriocheir sinensis microRNA transcriptome from claw muscles related to molting	DOI	`SRR7990528`	RNA-seq	Eriocheir sinensis	Muscle	Post-molt, pre-molt, and inter-molt stages (runs `SRR7990528`–`SRR7990530`)	29 Gb	Molting
Comparative transcriptomic analysis of late embryogenesis of the red claw crayfish	DOI	`PRJNA577772`	RNA-seq	Cherax quadricarinatus	Whole embryo	Three time points: 20, 27, and 35 days after fertilization	10 Gb	Embryogenesis
Transcriptomic analysis of Litopenaeus vannamei muscle in response to low-temperature stress	DOI	`SRP095377`	RNA-seq	Litopenaeus vannamei	Muscle	3 replicates × 4 groups (control, 13 °C 2 h, 13 °C 48 h, recovery)	59.2 Gb	Temperature response
Transcriptomic and histological analysis of oriental river prawn tissues in response to chronic hypoxia	DOI	`SRP056408`	RNA-seq, histology	Macrobrachium nipponense	Muscle, Gill	Hepatopancreas, muscle, and gill tissue from 6 prawns	22 Gb	Chronic hypoxia
Omics data on early molecular response underlying limb regeneration in the Chinese mitten crab	DOI	`PRJNA737102`	Genome, RNA-seq	Eriocheir sinensis	Muscle	Genome assembly from male muscle; limb-regeneration RNA-seq time-course (also `PRJNA733310`, `PRJNA480555`, NGDC `CRA003690`)	90 Gb + 64 Gb	Regeneration
Transcriptomic analysis across crayfish claw regeneration reveals potential stem cell sources for cultivated crustacean meat	DOI	`PRJNA780617`	RNA-seq	Cherax quadricarinatus	Regenerating claw (limb)	Bulk RNA-seq across six claw-regeneration stages, four pre-molt and two post-molt (Musgrove et al. 2024, International Journal of Molecular Sciences); 22 sequenced samples; pre-molt tissue upregulates stem-cell potency and growth-factor-receptor genes (Sox2, Klf4, C-Myc, FGFR, EGFR, PCNA), proposed as a non-lethal stem-cell source for cultivated crustacean meat; relative expression also hosted on CrustyBase	—	Regeneration & stem-cell sourcing
scRNA-seq of Penaeus japonicus hemocytes under environmentally-induced restriction of sand-diving behavior	DOI	`CRA030323`	scRNA-seq	Penaeus japonicus	Hemocytes	scRNA-seq of kuruma shrimp hemocytes across sandy, sandless, and sandless-stress groups (Zhang et al. 2025, Genomics); 13 subpopulations covering granular, semi-granular, hyaline, prohemocyte-like, and functional cells; restriction of natural sand-diving behavior reshapes hemocyte expression, with trpa1, trpm, and cut-family candidates; six sequencing runs across three biosamples	155 Gb	Single-cell atlas & stress response
Transcriptomic study of WSSV infection in Litopenaeus vannamei lymphoid organ via single nuclei RNA sequencing	DOI	`PRJNA1307069`	snRNA-seq	Litopenaeus vannamei	Lymphoid organ	First penaeid lymphoid-organ cell atlas, built by snRNA-seq after WSSV challenge of 32 adult shrimp via feed and injection (Florea et al. 2026, PLOS ONE); 18,541 nuclei after QC; introduces a shrimp-optimized nuclei-isolation protocol and flags candidate genes as CRISPR targets for WSSV-resistant stocks; 8 BioSamples (SAMN50653283–SAMN50653290)	—	Single-cell atlas & disease response

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.