Chicken is a leading cultivated-meat target — cultivated chicken was among the first products to reach regulatory approval — and Gallus gallus is among the first non-mammalian livestock species to gain a GTEx-style atlas. This page collects the fixed data artifacts relevant to cultivated chicken: the chicken genome-scale metabolic model, the multi-tissue atlases, and individual deposits spanning fibroblast immortalization for serum-free production, myogenesis, and skeletal-muscle development.
Chicken sub-portal of the FarmGTEx consortium — multi-tissue genetic-regulation maps across chicken tissues, the first GTEx-style resource for a non-mammalian amniote livestock species and directly useful for cultivated-chicken cell-line engineering. Companion to Papers.md ref #136 (Guan et al. 2025, Nature Genetics). 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-chicken developmental-biology and lineage-engineering work. 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 chicken reconstruction below inherits network structure from the human reference GEMs catalogued in HumanReference.md.
Generic genome-scale metabolic reconstruction of chicken, published 2022 in PLOS ONE by Salehabadi, Motamedian, and Shojaosadati. Contains 2,427 reactions across 1,300 genes (hence the i...1300 name); used to investigate network connectivity and identify potential biomarkers across chicken tissues. A generic chicken GEM that serves as a starting point for cultivated-chicken cell-line metabolic modelling, with SBML files provided as supplementary data.
Reference: Papers.md #82 (Salehabadi, Motamedian, & Shojaosadati 2022, PLOS ONE).
The most directly cultivated-meat-relevant chicken dataset profiles the spontaneous immortalization of chicken fibroblasts into stable, high-yield cell lines for serum-free cultured-meat production (GSE169291, Nature Food) — RNA-seq of primary and immortalized fibroblasts from two chicken breeds (Broiler Ross 308, Israeli Baladi). Immortalized, serum-free-adapted lines are a central enabling technology for cultivated chicken, and this is one of the few public datasets characterising that transition. The Tufts/Kaplan lab’s Contreras et al. 2026 (Food Research International, PRJNA1331774) extends this substrate from immortalization to scalable bioprocess geometry: time-series RNA-seq of the chicken embryonic-fibroblast DF-1 line transitioning from adherent to suspension culture identifies a putative MAPK p38δ–TEAD/YAP/FoxO1 mechanism for suspension proficiency — a critical trait for the high-density, low-handling cultures cultivated-chicken bioprocesses depend on.
Two datasets probe the myogenic program and its modulation. RNA-seq of chicken myoblasts under betaine treatment (CRA006598) examines nutrient regulation of myogenesis, and RNA-seq of broiler satellite cells under hypoxic culture (GSE241619) shows how oxygen tension shifts the balance between proliferation and differentiation — both directly relevant to media and bioprocess design for cultivated chicken. An earlier RNA-seq study of TP63 isoform regulation in chicken skeletal muscle differentiation (Luo et al. 2018, Frontiers in Physiology, GSE114452) adds a transcription-factor-level layer to the chicken myogenesis substrate, showing opposite roles for TP63 transcripts in myoblast proliferation vs differentiation.
Two further datasets build reference profiles of chicken skeletal muscle: a comprehensive expression survey of specific chicken skeletal muscles (SRP374834, Scientific Data) and a dynamic dual time-series comparing fast-growing Arbor Acres broilers with slow-growing Lushi chickens across embryonic and post-hatch stages (PRJNA729271).
A cluster of conventional-poultry omics studies complements the cultivated-chicken cell deposits above by characterising the muscle biology and quality defects of fast-growing broilers. Wooden breast — a fibrotic myopathy of modern broiler pectoralis major — is profiled at the transcriptome level by Mutryn et al. 2015 (BMC Genomics, NCBI PRJNA563347), the founding RNA-seq characterisation of the disorder, and at the metabolome level by Abasht et al. 2016 (PLOS ONE), whose untargeted GC/MS + LC/MS profiling links oxidative stress and metabolic perturbation to the phenotype. Both come from the same University of Delaware group and together map a growth-related muscle defect directly relevant to engineering cultivated-chicken muscle without analogous fibrosis. A separate authentication resource (Häfner et al. 2021, Food Control) provides validated HPLC-MS/MS marker peptides discriminating nine poultry species — a proteomic species-identification reference rather than a muscle-biology dataset. Serum and muscle ¹H- and ³¹P-NMR metabolomics of broiler lines divergently selected for ultimate pH (Beauclercq et al. 2016, Journal of Proteome Research) adds a metabolome layer aimed at predicting ultimate pH, a key determinant of chicken-meat quality.
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 |
|---|---|---|---|---|---|---|---|
| Spontaneous immortalization of chicken fibroblasts generates stable, high-yield cell lines for serum-free production of cultured meat | DOI | GSE169291 | RNA-seq | Embryo | Primary and immortalized fibroblasts from 2 chicken breeds (Broiler Ross 308; Israeli Baladi), 3 replicates each | 163.68 Gb | Cultured meat |
| Comparative transcriptomics of adherent and suspension chicken fibroblast cell lines for the optimization of cultivated meat processes | DOI | PRJNA1331774 | RNA-seq (time-series) | Cell line (DF-1 chicken embryonic fibroblast) | Time-series RNA-seq of the DF-1 chicken embryonic-fibroblast line transitioning from adherent to suspension culture, 5 timepoints × 4 replicates (20 paired-end Illumina runs); identifies a putative MAPK p38δ–TEAD/YAP/FoxO1 mechanism for suspension proficiency (Tufts/Kaplan lab; Contreras, Nagarajan, Bromberg, Villegas, & Kaplan 2026, Food Research International) | 145.44 Gb | Cultured meat / suspension cell-line adaptation |
| RNA sequencing reveals the regulation of betaine on chicken myogenesis | DOI | CRA006598 | RNA-seq | Muscle | 12 myoblast-cell samples, 3 replicates per betaine treatment | 69.12 Gb | Chicken myogenesis |
| Gene expression profiles of specific chicken skeletal muscles | DOI | SRP374834 | RNA-seq | Muscle | 4 or 6 biological replicates of each skeletal muscle | 418.4 Gb | Chicken skeletal muscle |
| Comparative analyses of dynamic transcriptome profiles for muscle development and growth in chicken | DOI | PRJNA729271 | RNA-seq | Muscle | Breast-muscle time-series of fast-growing Arbor Acres and slow-growing Lushi chickens at E10/14/18, post-hatch d1, w1/3/5 | 605 Gb | Breast-muscle development |
| Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells | DOI | GSE241619 | RNA-seq | Muscle | Pectoralis-major satellite cells under hypoxic culture, harvested 0/12/24/36/48 h after differentiation | 4 Gb | Muscle growth |
| TP63 Transcripts Play Opposite Roles in Chicken Skeletal Muscle Differentiation | DOI | GSE114452 | RNA-seq | Muscle (primary myoblasts) | Chicken primary myoblasts transfected with TAp63α or 1Np63α overexpression vectors vs GFP control; the two TP63 isoforms show opposing proliferation/differentiation roles | — | TF regulation of myogenesis |
| Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing | DOI | PRJNA563347 | RNA-seq | Muscle (pectoralis major) | Broiler P. major RNA-seq, wooden-breast disorder vs unaffected, with differential-expression + pathway analysis (Mutryn et al. 2015, BMC Genomics); Illumina | 11 SRA runs | Wooden breast / muscle disorder |
| Oxidative stress and metabolic perturbations in wooden breast disorder in chickens | DOI | supplementary | Untargeted metabolomics (GC/MS + LC/MS) | Muscle (pectoralis major) | Untargeted metabolome of wooden-breast-affected vs unaffected broiler breast across genetic lines (Abasht et al. 2016, PLOS ONE); full metabolite quantification table (282 compounds of known identity with CAS/HMDB/KEGG/PubChem IDs) released as open Supporting Information (S2 File) — supplementary data, not a repository deposit | — | Wooden breast / metabolomics |
| Authentication of nine poultry species using high-performance liquid chromatography–tandem mass spectrometry | DOI | supplementary | HPLC-MS/MS (targeted marker peptides) | Muscle (nine poultry species) | Species-specific tryptic marker peptides discriminating nine poultry species incl. chicken, turkey, duck, and goose (Häfner et al. 2021, Food Control); validated marker-peptide tables released as open supplementary files (Table S3) — supplementary data, not a repository deposit | — | Meat-species authentication |
| Serum and muscle metabolomics for the prediction of ultimate pH, a key factor for chicken-meat quality | DOI | supplementary | ¹H / ³¹P-NMR metabolomics | Serum + muscle | Broiler lines divergently selected for ultimate pH (Beauclercq et al. 2016, Journal of Proteome Research); ¹H-NMR spectra plus a compiled ³¹P-NMR chemical-shift database of muscle metabolites and enrichment-test tables in ACS Supporting Information — supplementary data, not a repository deposit | — | Meat-quality metabolomics |
| Dataset of the application of handheld NIR and machine learning for chicken fillet authenticity study | DOI | Mendeley | NIR spectroscopy (handheld) | Muscle (breast fillet) | Handheld MicroNIR near-infrared spectra of chicken breast fillets across countries and growth conditions for a “Measure & Monitor” authenticity classifier (van Kollenburg et al. 2020, Data in Brief; companion to the Food Control source study 10.1016/j.foodcont.2020.107149; Mendeley v6) | — | Meat authenticity NIR |
| Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens | DOI | PRJNA1017808 | Spatial transcriptomics (10x Visium) | Muscle (pectoralis major) | 10x Visium spatial transcriptomics of pectoralis major from three broilers (Cobb500) at 23 days post-hatch, resolving lipid-laden macrophages, myositis, vasculature, and unaffected myofibers in early wooden-breast onset (Wang, Khondowe, Brannick & Abasht 2024, Scientific Reports) | 3 broilers | Wooden breast / muscle disorder |
| An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics | DOI | PRJEB55656 | ChIP-seq + ATAC-seq + DNase-seq + RNA-seq + RRBS + Hi-C | 23 adult tissues | Multi-assay regulatory atlas integrating 377 datasets across 23 adult chicken tissues (ChIP-seq for H3K4me3/H3K4me1/H3K27ac/H3K27me3/CTCF, ATAC-seq, DNase-seq, RNA-seq, RRBS, Hi-C), annotating ~1.57 M regulatory elements across 15 chromatin states; 15 tissues newly generated, also reusing the FAANG pilot GEO GSE158430 (Pan et al. 2023, Science Advances) | 377 datasets | Regulatory-element annotation |
Curation source: The cultured-cell, myogenesis, and muscle-development deposits 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 muscle-disorder, meat-quality & authentication entries were 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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