Pig / Sus scrofa

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.

Featured atlases

PigGTEx-Portal

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.

GENE-SWitCH

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.

PigBiobank

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.

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 porcine reconstruction below inherits network structure from the human reference GEMs catalogued in HumanReference.md.

pcPigMNet2025 — Sus scrofa (porcine)

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).

Embryonic & developmental myogenesis

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.

Single-cell cellular landscape & muscle evolution

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.

Marbling, lipid metabolism & adipogenesis

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.

Epigenomics, chromatin & cultured-meat tissue

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.

Postmortem proteome & meat-quality omics

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.

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	Type	Tissue	Description	Size	Area of research
Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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.