Cross-species reference substrate

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

Growth factor thermostability dataset

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.

Cell culture media component characterization

NMR metabolomics of plant and yeast-based hydrolysates

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.

Plant-based meat compositional & textural reference

Plant-based meat textural-properties training table (Kircali Ata et al. 2023)

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.

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 (per Current Research in Food Science open-access default)
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)

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 — integrated muscle-regeneration scRNA reference whose transitional-progenitor labels are reusable as a cross-species template.
  • 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.