Pigs are a major cultivated-meat target and, via the FarmGTEx pig effort, one of the best-characterized livestock species at the systems-genetics level. This page collects the fixed data artifacts relevant to cultivated pork: the porcine muscle-stem-cell genome-scale metabolic model, the multi-tissue atlases, and individual deposits spanning myogenesis, the cellular landscape of skeletal muscle, marbling and intramuscular-fat biology, and 3D meat-like tissue work.
Pig sub-portal of the FarmGTEx consortium — multi-tissue expression QTL (eQTL), splice QTL (sQTL), and related molecular-QTL maps across pig tissues. Companion to Papers.md ref #135 (Teng et al. 2024, Nature Genetics); see also Papers.md / Livestock Functional Genomics Reference Work for the full PigGTEx-family citations (refs #135, #139–#142). Full entry in Databases.md / Livestock Multi-Tissue Atlases.
The FAANG consortium’s pig + chicken project — the regulatory GENomE of SWine and CHicken: functional annotation during development; the data hub hosts its open releases. Substrate for cultivated-pork developmental-biology and lineage-engineering work. Full entry in Databases.md / Livestock Multi-Tissue Atlases.
Trait-data biobank coordinated with PigGTEx, integrating phenotypic, genotypic, and expression data on diverse pig traits — complementary to PigGTEx-Portal’s molecular-QTL focus. Not part of the Todhunter 2024 supplemental; included here as a CAAIL-curated pig resource. Companion to Papers.md ref #139 (Zeng et al. 2024, Nucleic Acids Research). Full entry in Databases.md / Livestock Multi-Tissue Atlases.
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 porcine reconstructions below inherit network structure from the human reference GEMs catalogued in HumanReference.md.
pcPigMNet2025 is the first proteome-constrained metabolic model for the core metabolism of Sus scrofa muscle stem cells, published 2026 in Metabolic Engineering by Qiu et al. — a University of Oxford collaboration with Ivy Farm Technologies, funded by the UK Biotechnology and Biological Sciences Research Council (UKRI). It constrains a base reconstruction (PigMNet2025) with enzyme-activity data to simulate how accumulated lactate and ammonium inhibit muscle-stem-cell growth and metabolism during the proliferation step of cultivated-pork production — a model-aided process-engineering tool for controlling and optimising culture conditions. SBML files are released alongside the paper.
Reference: Papers.md #83 (Qiu et al. 2026, Metabolic Engineering).
iSsus3744 is a genome-scale metabolic reconstruction for Sus scrofa, presented in a 2026 bioRxiv preprint by Gomez Romero et al. (Colorado School of Mines / Cultivated Meat Modeling Consortium). It was reconstructed from the HumanGEM and Recon3D human reference models by orthology mapping (using the RAVEN and COBRA toolboxes) and applied to rational media design for cultivated pork, using constraint-based metabolic flux analysis to reason about the medium components that govern porcine cell metabolism. Where pcPigMNet2025 above is a proteome-constrained model of core muscle-stem-cell metabolism, iSsus3744 is a whole genome-scale reconstruction oriented toward media-formulation design. The reconstruction is distributed with the preprint as supplemental files (the model as Supplemental File 1, its reactions and metabolites in Supplemental Files 2–3) rather than through a model repository — there is no BioModels or GitHub deposit and no formal data-availability statement.
Reference: Papers.md #240 (Gomez Romero et al. 2026, bioRxiv).
The largest pig data cluster tracks skeletal-muscle formation from embryo to postnatal growth — the developmental program a cultivated-pork process aims to recapitulate in vitro. Integrative scRNA-seq + ATAC-seq of somites and myotomes (GSE206914), chromatin-accessibility profiling of embryonic skeletal muscle at 45/70/100 days post coitus (CRA003275), and prenatal comparative transcriptomics of Tongcheng vs Yorkshire pigs (SRP066398) resolve the embryonic stages, while single-cell profiling of satellite cells and myoblasts (PRJNA852173), postnatal transcriptome dynamics in Tibetan piglets (PRJNA527944), and a developmental-stage × genotype transcriptome study (GSE86441) extend the picture into postnatal growth.
A second cluster builds single-cell references of porcine skeletal muscle. A cellular landscape of the longissimus dorsi in a newborn Suhuai pig (GSE247753) and a cross-breed single-cell study spanning wild boars, Laiwu, and Duroc pigs (CRA011788) characterise the cell-type composition and its evolutionary divergence under domestication and selection; a scRNA-seq + proteomics association study of Ca²⁺ signalling in muscle-development potential is listed in the inventory though the source survey records no data accession for it.
Intramuscular fat is a central quality target for cultivated pork. Single-nucleus and bulk RNA-seq with lipidomics of high- vs low-marbled Laiwu pork (CRA011059/CRA011069), a longissimus-dorsi IMF transcriptome of 28 Duroc pigs (PRJNA527944), a lncRNA–mRNA time-series of adipogenic transdifferentiation of porcine satellite cells (PRJNA820138), and a Luchuan-vs-Duroc lipidomic/transcriptomic comparison (data in the paper’s supplementary Table 1) together map the adipogenic program and the cell-fate switch between myogenesis and adipogenesis. An integrated lipidomic + transcriptomic comparison of cultured fat from porcine subcutaneous pre-adipocytes (SAT) vs fibro-adipogenic progenitors (FAPs) in a KA-hydrogel 3D culture (Gu et al. 2026, Food Chemistry) extends the cluster into directly in-vitro cultivated-fat substrate, identifying cell-type-specific phospholipid and ceramide signatures relevant to seed-cell selection. A more recent Roslin Institute / Edinburgh data paper (Thrower et al. 2026, Data in Brief, GSE271977 / PRJNA1134234) releases a bulk RNA-seq dataset across clonal porcine adipose-derived MSC populations sorted by FACS and classified by Oil-Red-O-scored adipogenic capacity — useful substrate for benchmarking adipogenic-potential prediction in cultivated-pork MSC lines.
The final cluster covers regulatory-genome and cultured-tissue work: integrative ATAC-seq + RNA-seq of Luchuan vs Duroc longissimus muscle (GSE180840), H3K27me3 ChIP-seq during porcine satellite-cell differentiation (SRP180031/SRP180432), the multi-species functional-annotation effort (GSE158430, which also covers cattle — see Cow.md), and a multi-breed multi-omics characterisation of growth traits across Duroc, Landrace, and Yorkshire pigs (Zhao et al. 2026, BMC Genomics) that integrates three-method GWAS (MLM, FarmCPU, BLINK) with RNA-seq, ATAC-seq, and ChIP-seq to identify ARL8A as a candidate gene conserved between Duroc and Yorkshire (not Landrace) that regulates backfat thickness and loin-eye area — new genome-variation data deposited at the CNCB Genome Variation Map (GVM001420). Most directly cultivated-meat-relevant is the generation of three-dimensional meat-like tissue from stable pig epiblast stem cells (GSE223433, with companion metabolome data), a rare in-vitro cultured-tissue dataset.
Water-holding capacity (WHC) — how much moisture pork retains postmortem — is a defining textural quality trait cultivated pork must reproduce. A 2D-DIGE proteomic study of porcine muscle exudate (di Luca et al. 2016, PLOS ONE) compares divergent water-holding phenotypes across the postmortem aging period, identifying sarcoplasmic and metabolic proteins associated with drip loss; a TMT-based quantitative proteome of high- versus low-quality porcine longissimus (Hou et al. 2020, Food Chemistry) extends the cluster to general postmortem meat quality with a full ~1011-protein quantification. Both are reference substrate for proteomic quality-prediction relevant to cultivated-pork texture (see Sensory Prediction); neither deposited to a repository — their data tables are in the papers’ supplementary materials.
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 | Tissue | Description | Size | Area of research |
|---|---|---|---|---|---|---|---|
| Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig | DOI | GSE206914 | scRNA-seq + ATAC-seq | Muscle | Somites and myotomes at E18, E21, E28 from Tibetan and Duroc×Tibetan pigs | 599.17 Gb | Skeletal muscle ontogeny |
| Single-cell transcriptional profiling of porcine muscle satellite cells and myoblasts during myogenesis | DOI | PRJNA852173 | scRNA-seq | Muscle | Longissimus dorsi from 3-day-old piglets | 86 Gb | Porcine muscle myogenesis |
| Single-cell RNA sequencing reveals the cellular landscape of longissimus dorsi in a newborn Suhuai pig | DOI | GSE247753 | scRNA-seq | Muscle | Longissimus dorsi muscle cell atlas of a 1-day-old Suhuai pig | 69.76 Gb | Meat quality |
| Single-cell RNA-sequencing provides insight into skeletal muscle evolution during the selection of muscle characteristics | DOI | CRA011788 | scRNA-seq | Muscle | 60,040 cells from wild boars, Laiwu pigs, and Duroc pigs | 357.09 Gb | Skeletal muscle evolution |
| Single-nucleus and bulk RNA sequencing reveal mechanisms underlying lipid dynamics in high-marbled pork | DOI | CRA011059 | snRNA-seq + RNA-seq + lipidomics | Fat | Laiwu pigs with high vs low intramuscular fat (also CRA011069) | 95.95 Gb | Lipid metabolism, marbling |
| Integrative ATAC-seq and RNA-seq analysis of the longissimus muscle of Luchuan and Duroc pigs | DOI | GSE180840 | RNA-seq + ATAC-seq | Muscle | Longissimus muscle of 180-day-old Duroc and Luchuan pigs | 191.21 Gb | Muscle-fibre differences |
| H3K27me3 depletion during differentiation promotes myogenic transcription in porcine satellite cells | DOI | SRP180031 | RNA-seq + ChIP-seq | Muscle | Satellite cells from hind-leg muscles of one-week-old Yorkshire male piglets (also SRP180432) | 95.5 Gb | Epigenomic myogenesis |
| The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs | DOI | CRA003275 | RNA-seq + ATAC-seq | Muscle | Skeletal muscle from pig embryos at 45, 70, 100 days post coitus | 205.41 Gb | Embryonic muscle development |
| Comparative transcriptomic analysis of skeletal muscle during prenatal stages in Tongcheng and Yorkshire pig | DOI | SRP066398 | RNA-seq | Muscle | Skeletal muscle, Tongcheng vs Yorkshire, at 40/55/63/70/90 d gestation | 69.7 Gb | Transcriptional regulation of myogenesis |
| Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development | DOI | PRJNA527944 | RNA-seq | Muscle | 12 longissimus dorsi samples from Tibetan piglets at 0/14/30/60 d; shares BioProject PRJNA527944 with the Duroc IMF study below (same research group) | 269 Gb | Postnatal transcriptome dynamics |
| Muscle transcriptome analysis reveals candidate genes and pathways affecting intramuscular fat content in pigs | DOI | PRJNA527944 | RNA-seq | Muscle | Longissimus dorsi transcriptomes of 28 purebred Duroc pigs; shares BioProject PRJNA527944 with the postnatal-development study above (same research group) | 269 Gb | Intramuscular fat content |
| Developmental stage, muscle and genetic type modify muscle transcriptome in pigs | DOI | GSE86441 | RNA-seq | Muscle | 24 longissimus dorsi samples, Iberian and Iberian×Duroc newborns at birth and 4 months | 153.05 Gb | Gene expression during development |
| Time-series clustering of lncRNA-mRNA expression during adipogenic transdifferentiation of porcine skeletal muscle satellite cells | DOI | PRJNA820138 | RNA-seq | Muscle, Fat | 4 timepoints during adipogenic transdifferentiation | 144.9 Gb | Adipogenesis and cell fate |
| Lipidomic and transcriptomic analysis of the longissimus muscle of Luchuan and Duroc pigs | DOI | supplementary | RNA-seq | Muscle, Fat | 6 Luchuan and Duroc boar pigs at 180 days; data in the paper’s supplementary Table 1 (no repository accession) | — | Intramuscular fat between breeds |
| Functional annotations of three domestic animal genomes | DOI | GSE158430 | ChIP-seq + ATAC-seq | 8 tissues incl. skeletal muscle, adipose | ATAC-seq and CTCF ChIP-seq across 8 tissues; one multi-species GEO deposit, also covers cattle (see Cow.md) | 4.28 B ChIP-seq + 1.04 B ATAC-seq reads (pig-relevant figure from the source survey) | Comparative epigenomics |
| Association analysis of single-cell RNA sequencing and proteomics reveals a vital role of Ca²⁺ signalling in skeletal muscle development potential | DOI | unavailable | scRNA-seq | Muscle | Source survey records no data accession | — | Myogenesis–adipogenesis homeostasis |
| Generation of three-dimensional meat-like tissue from stable pig epiblast stem cells | DOI | GSE223433 | RNA-seq + mass spectrometry | Muscle | Pig stem cells at P30, P200, and during myogenic differentiation; includes metabolome data (also OMIX005128) | 95 Gb | Muscle development |
| Integrated lipidomics and transcriptomics of cultured fat from porcine SAT vs fibro-adipogenic progenitors | DOI | supplementary | RNA-seq + lipidomics (LC-MS) | Fat (cultured) | Cultured fat produced from porcine subcutaneous pre-adipocytes (SAT) vs fibro-adipogenic progenitors (FAPs) in a KA-hydrogel 3D system; 14-day adipogenic differentiation; lipidomics n=6 / transcriptomics n=4 per group; no public repository accession — processed data in the paper’s supplementary materials | — | Cultured fat & seed-cell selection |
| Multi-omics characterization identifies conserved candidate gene and reveals breed-specific regulatory mechanisms underlying growth-related traits in pigs | DOI | GVM001420 | GWAS + RNA-seq + ATAC-seq + ChIP-seq | Muscle, Fat | Duroc, Landrace, and Yorkshire pigs (with a Meishan reference); growth traits ADG, AGE, BF, LEA; identifies ARL8A as a conserved candidate gene. New genome-variation data at CNCB Genome Variation Map GVM001420; reuses public SRA PRJNA597497 and PRJNA287471 | — | Growth traits & multi-breed regulation |
| A transcriptome dataset from porcine stem cells with differing adipogenic capacity | DOI | GSE271977 | RNA-seq | Fat (adipose-derived MSCs) | Clonal porcine adipose-derived MSC populations FACS-sorted to single cells and phenotyped by Oil Red O scoring after differentiation, classified as high vs low adipogenic capacity (Roslin Institute / Edinburgh); NCBI GEO GSE271977 / BioProject PRJNA1134234 | — | Adipogenic capacity benchmarking |
| Cost-effective production of meaty aroma from porcine cells for hybrid cultivated meat | DOI | on request | RNA-seq | Cell line (porcine myoblasts and fibroblasts) | RNA-seq across four adaptation stages of spontaneously immortalized porcine myoblast and fibroblast cell lines — primary, immortalized adherent, immortalized full-serum suspension, and immortalized low-serum suspension (n=3 per stage); PCA + hierarchical clustering against 19 public SRA BioProjects confirms cell identity throughout the suspension-adaptation pipeline. Companion to Papers.md #193 (Zhou et al. 2025, Food Chemistry); no public repository accession — data available on request per the paper’s data availability statement | — | Suspension cell-line adaptation & cultivated-pork bioprocess |
| Comparative proteomic profiling of divergent phenotypes for water holding capacity across the Post Mortem ageing period in porcine muscle exudate | DOI | supplementary | 2D-DIGE proteomics | Muscle (centrifugal drip / exudate) | Divergent water-holding (drip-loss) phenotypes in porcine centrifugal drip (longissimus thoracis et lumborum) across postmortem aging days 1/3/7 (di Luca et al. 2016, PLOS ONE); the identified protein/fragment-spot table (59 unique proteins with UniProt IDs) is available as open Supporting Information (S1 Table); the paper’s original UCD-2DPAGE database deposit is no longer reachable | — | Postmortem proteome & water-holding capacity |
| TMT-based quantitative proteomic analysis of porcine muscle associated with postmortem meat quality | DOI | supplementary | TMT LC-MS/MS proteomics | Muscle (longissimus) | High- vs low-quality porcine longissimus (4 vs 4) postmortem (Hou et al. 2020, Food Chemistry); full ~1011-protein quantification table, 140 differentially expressed proteins, and GO/KEGG enrichment in Supplementary Tables S1–S3 — supplementary data, not a repository deposit | — | Postmortem proteome & meat quality |
| snRNA-Seq and spatial transcriptome reveal cell-cell crosstalk mediated metabolic regulation in porcine skeletal muscle | DOI | supplementary | snRNA-seq + spatial transcriptomics | Muscle (skeletal) | Single-nucleus RNA-seq plus spatial transcriptome of porcine skeletal muscle mapping cell-cell crosstalk that mediates metabolic regulation; the data-availability statement places raw sequence data in ScienceDB with no accession named, and states evaluation data are in the paper and Supporting Information | — | Muscle metabolism & cell-cell signalling |
| Pig genome functional annotation enhances the biological interpretation of complex traits and human disease | DOI | GSE158430 | ChIP-seq + ATAC-seq + RNA-seq + RRBS | 8 tissues (incl. skeletal muscle, adipose) | Pig functional-genome annotation across tissues (regulatory elements, chromatin states) enhancing interpretation of complex traits; eight-tissue data at GEO GSE158430, six gut tissues at ENA PRJEB37735, RRBS methylomes at ENA PRJNA762083, all also on the FAANG data portal | — | Regulatory genomics & functional annotation |
| Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions | DOI | PRJEB41485 | ATAC-seq + RNA-seq | Muscle (fetal skeletal, day-90 gestation) | Open-chromatin (ATAC-seq, n=24) and matched RNA-seq (n=26) of developing pig muscle in large- vs small-sized day-90 fetal piglets to identify muscle regulatory regions; ATAC-seq at ENA PRJEB41485, RNA-seq at ENA PRJEB41488 | — | Developmental regulatory genomics |
| Tecator NIR meat spectra (Infratec Food and Feed Analyzer benchmark) | none named | OpenML-505 | NIR transmission spectra (850-1050 nm) | Meat (finely chopped pure meat) | Classic NIR spectroscopy regression benchmark: 100-channel near-infrared absorbance spectra of finely chopped pure-meat samples with lab-measured fat, moisture, and protein, recorded on a Tecator Infratec analyzer; a compact public-domain testbed for spectral fat/moisture/protein prediction relevant to cultivated-pork composition QC | 240 samples | Sensory & quality prediction (NIR spectral benchmark) |
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. The postmortem proteome & water-holding-capacity entry was curated by walking the cited references of the Encyclopedia of Meat Sciences (2024) reviews on proteomics (Gagaoua et al. 2024) and metabolomics (Kiyimba et al. 2024) in meat research.
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