Cellular agriculture programs share a layer of engineering substrate that spans species — recombinant growth factors, media-component reference data, screening assays, and related resources whose utility is not tied to a single cultivated-meat species. This page collects the fixed data artifacts in that cross-species layer: entries here apply across livestock, poultry, and aquaculture programs simultaneously, rather than fitting any one per-species page.
The page sits beside HumanReference.md and CHOReference.md, which together hold cross-species reference biology — single-cell pretraining corpora and the human and CHO genome-scale metabolic models from which livestock GEMs inherit network structure. CrossSpecies.md complements those reference-biology pages with cross-species engineering substrate — protein-engineering and media-optimization data that cultivated-meat programs reuse across species.
Protein engineering & growth factor reference
The Ng et al. 2026 Zenodo deposit (DOI 10.5281/zenodo.19339684, CC-BY-4.0) is a 513-value catalogue of melting-temperature measurements across growth factors and variants commonly used in cultured meat and seafood production. The dataset combines experimentally measured thermal-shift values with computationally predicted thermostability data; the literature-review component was assembled via a two-stage LLM-assisted workflow (DeepSeek first-pass extraction, then GPT-4.1 refinement after a manual-check step, per the companion repo’s README) and is paired with novel thermal-shift measurements. A 15-growth-factor subset additionally carries in silico thermodynamic parameters derived from FoldX. Distributed as a single Growth_Factor_Thermostability.xlsx (93.2 kB). The Zenodo record’s description frames the dataset as broadly applicable to “cultured meat and seafood production” and does not summarize species coverage at the record level — the spreadsheet itself carries a per-row Species Origin column. Companion data for the amii-cell-ag-tools / protein-thermostability-data-tools module — see Software.md / amii-cell-ag-tools.
The Combe et al. 2024 Current Research in Food Science paper is a comprehensive NMR-metabolomics characterization of plant- and yeast-based hydrolysates intended as serum-free media components for cultivated meat. Hydrolysates are one of the dominant valorized-substrate strategies for replacing the 55–95% media-cost component that fetal bovine serum currently fills, but their composition varies sharply by source, and that variability is precisely what NMR-based metabolite profiling can resolve. Catalogued here on CrossSpecies.md because hydrolysate selection is a media-substrate question that any cultivated-meat program — bovine, porcine, avian, aquaculture — addresses, and the per-source NMR profiles in this work are reusable across species.
cited by7
Plant-based meat compositional & textural reference
A small tabular dataset linking proximate composition (% protein, fat, carbohydrate, fibre, ash, moisture) plus a “targeted moisture content” feature to the measured textural properties of plant-based meat analogs. Generated by Kircali Ata et al. (2023, Foods 12(2), 344) to train Ridge, XGBoost, and related regressors for analog-texture prediction, which places Papers.md #171 in the matrix’s Ensemble Learning × Sensory Prediction cell. Catalogued on CrossSpecies.md because the dataset is a generic plant-protein-formulation substrate that any hybrid cultivated-meat program reuses regardless of target species. Distributed only as supplementary material with the paper — no public repository accession.
cited by29
Cross-species regulatory & functional-genomics reference
The Foissac et al. 2019 BMC Biology paper is the first FAANG multi-species, multi-assay genome annotation: RNA-seq, ATAC-seq, and in situ Hi-C on liver and CD4+/CD8+ T cells from cattle, goat, chicken, and pig. It extends each species’ transcript catalog, maps accessible chromatin and transcription-factor-enriched regulatory regions, and annotates topological domains and A/B compartments, showing a conserved core of regulatory architecture across the four livestock species. Catalogued here because it is a genuinely cross-species regulatory substrate: the same annotation layer supports seed-cell and engineering work in bovine, porcine, and avian programs alike. Raw data at ENA / the FAANG Data Coordination Center under PRJEB27455 (RNA-seq), PRJEB27111 (ATAC-seq), and PRJEB27364 (Hi-C).
cited by194
The Halstead et al. 2020 BMC Genomics study builds consensus and tissue-specific open-chromatin (ATAC-seq) maps for cattle, pig, and mouse and evaluates conservation of accessible regions across the three species via the EPO whole-genome alignment. It is a cross-species regulatory reference for identifying candidate cis-regulatory elements in livestock where functional annotation is sparse, transferable across cultivated-meat species. New cattle and pig ATAC-seq are at ENA PRJEB14330; the mouse ATAC-seq was reused from CNGB CNP0000198.
cited by84
Fungal (mycelium) meat texture reference
The Vervenne et al. 2025 Acta Biomaterialia paper characterizes the mechanical, rheological, and taste properties of mycelium “fungi steak,” quantifying the moist, fibrous signature that makes fungal biomass a whole-cut meat analog. Catalogued here as a species-agnostic texture and scaffold reference: the target mechanical and sensory envelopes it reports are reusable across cultivated and fungal-meat programs regardless of animal species. Mechanical, rheological, and sensory data only; no sequencing deposit.
cited by10
The St. Pierre et al. 2026 bioRxiv preprint characterizes the mechanical, rheological, and sensory properties of a lion’s mane mushroom steak as a whole-cut analog, adding a second fungal texture reference alongside the fungi-steak work above. Not yet peer-reviewed. Species-agnostic (fungal), with texture and scaffold relevance across cultivated and fungal meats.
cited by0
Complete data inventory
| Resource | Year | Format | Scope | DOI / URL | License |
|---|
| Growth factor thermostability dataset (Ng et al.) | 2026 | XLSX (single file, 93.2 kB) | 513 melting-temperature values across growth factors and variants used in cultured meat/seafood; 15-protein FoldX in silico subset | 10.5281/zenodo.19339684 | CC-BY-4.0 |
| NMR metabolomics of plant and yeast-based hydrolysates (Combe et al.) | 2024 | NMR metabolite profiles | Comprehensive assessment of plant- and yeast-based hydrolysates intended as serum-free media components for cultivated meat; see paper’s data availability statement for accession | 10.1016/j.crfs.2024.100855 | CC-BY-NC-4.0 |
| Plant-based meat textural-properties training table (Kircali Ata et al.) | 2023 | Tabular (Supplementary) | Proximate composition (% protein/fat/carbohydrate/fibre/ash/moisture) + targeted moisture content → textural properties for plant-based meat analogs; training data for the Ridge / XGBoost / etc. regressors of Papers.md #171; no public repository accession | 10.3390/foods12020344 | CC-BY (per Foods MDPI open-access default) |
| FR-AgENCODE multi-species farm-animal regulatory atlas (Foissac et al.) | 2019 | RNA-seq + ATAC-seq + Hi-C (ENA / FAANG DCC) | First FAANG multi-species, multi-assay genome annotation across cattle, goat, chicken, and pig (liver + CD4+/CD8+ T cells): extended transcript catalogs, differentially accessible chromatin, and Hi-C TADs / A/B compartments, with a conserved core of regulatory regions. ENA accessions PRJEB27455 (RNA-seq), PRJEB27111 (ATAC-seq), PRJEB27364 (Hi-C) | 10.1186/s12915-019-0726-5 | CC-BY-4.0 (BMC Biology open access) |
| Comparative chromatin accessibility in cattle, pig, and mouse (Halstead et al.) | 2020 | ATAC-seq (ENA / CNGB) | Consensus and tissue-specific open-chromatin maps across cattle, pig, and mouse tissues, with interspecies conservation assessed via the EPO whole-genome alignment. New cattle + pig ATAC-seq at ENA PRJEB14330; mouse ATAC-seq reused from CNGB CNP0000198 | 10.1186/s12864-020-07078-9 | CC-BY-4.0 (BMC Genomics open access) |
| Mycelium mechanics & taste of fungi steak (Vervenne et al.) | 2025 | Mechanical + rheological + sensory/taste measurements | Fungal cell-ag texture reference: mechanical, rheological, and taste characterization of mycelium “fungi steak” as a whole-cut analog (its moist, fibrous signature), informing scaffold and texture targets reused across cultivated and fungal meats. Species-agnostic (fungal, not livestock); no sequencing deposit | 10.1016/j.actbio.2025.07.002 | Elsevier subscription/hybrid (license unverified) |
| Lion’s mane mushroom-steak characterization (St. Pierre et al.) | 2026 (preprint) | Mechanical + rheological + sensory measurements | Fungal cell-ag texture reference: mechanical, rheological, and sensory characterization of a lion’s mane mushroom steak as a whole-cut analog, with texture/scaffold relevance across cultivated and fungal meats. bioRxiv preprint (not yet peer-reviewed); species-agnostic (fungal) | preprint | bioRxiv preprint (author license unverified) |
Further reading
HumanReference.md and CHOReference.md for cross-species reference biology — single-cell pretraining corpora, human GEMs, and the CHO biopharma substrate that pair with the cross-species engineering substrate catalogued here.Software.md for applied AI research code that uses these artifacts, including amii-cell-ag-tools (whose protein-thermostability-data-tools module produced the Ng et al. dataset).- The per-species pages —
Cow.md, Pig.md, Chicken.md, Fish.md, and the others in this directory — for species-scoped deposits that complement the cross-species substrate here.
- Adjacent single-cell atlases & methods (cross-species):
- Ford et al. 2023, Biology, White Adipose Tissue Heterogeneity in the Single-Cell Era: From Mice and Humans to Cattle — cross-species review of single-cell white-adipose heterogeneity from mouse and human into cattle, directly relevant to cultivated-fat seed-cell selection across species.
- McKellar et al. 2021, Communications Biology, Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration — an integration of publicly available mouse skeletal-muscle scRNA-seq and snRNA-seq datasets into a harmonized regeneration reference whose transitional-progenitor labels are reusable as a cross-species template. The harmonized atlas, integration code, and curated muscle marker-gene lists (cell-type markers plus TF, surfaceome, and stress gene sets) are maintained in the open
mckellardw/scMuscle repository — a ready-made annotation and marker-set resource for labelling cultivated-muscle single-cell data.
- Liu et al. 2022, Genome Research, Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network — GNN-based cross-species cell-type assignment method addressing the labelled-data scarcity in non-model cultivated-meat species.
- Cardiello et al. 2023, Life Science Alliance, Evaluation of genetic demultiplexing of single-cell sequencing data from model species — benchmark of genotype-based demultiplexing tools across mouse/zebrafish/Drosophila, informing pooled-experiment design in cultivated-livestock species.
- Petrany et al. 2020, Nature Communications, Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers — companion to Papers.md #187; mouse skeletal-myofiber snRNA-seq (GEO
GSE147127, Synapse syn21676145, interactive portal research.cchmc.org/myoatlas) — the substrate methodology and reference data for cultivated-muscle myofiber single-cell work.
- Niu et al. 2026, Animal Genetics, A Cross-Species Single-Cell Transcriptomic Atlas of Subcutaneous Adipose Tissue Reveals Conserved and Divergent Cellular Programs — an integrative re-analysis of five publicly available scRNA-seq datasets spanning cattle (n = 6), pigs (n = 2), and humans (n = 5), drawn from public NCBI deposits (GEO
GSE281356, GSE241555, GSE193795, GSE264101, GSE211707), resolving a conserved subcutaneous-adipose cell-type framework (adipocytes, adipose stem and progenitor cells, macrophages, endothelial cells, T cells) across mammals — a cross-species reference for cultivated-fat seed-cell selection.