Raw data were processed using Compound Discoverer 3.3 (Thermo Fisher Scientific) for peak picking, retention time alignment, and normalization using Progenesis QI (Waters Corporation, Milford, MA). Multivariate analyses (Principal component analysis (PCA), OPLS DA) and differential metabolite identification (VIP > 1, log2FC ≥ 0.585, FDR < 0.05) were performed in the R environment using the ropls package (Bioconductor open-source project) (https://www.bioconductor.org/packages/release/bioc/vignettes/ropls/inst/doc/ropls-vignette.html the-ropls-package). Metabolites with FC (LSF/WLC) ≥ 1.5 and an adjusted p < 0.05 were classified as significantly upregulated in the LSF group.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Metabolites were separated on a Vanquish Ultra-performance liquid chromatography (UPLC; Thermo Fisher Scientific, Waltham, MA, USA) with a Waters Acquity UPLC HSS T3 column (100 × 2.1 mm, 1.8 µm) at 0.3 mL/min, 40 °C. Mobile phases A = 0.1% formic acid in water and B = 0.1% formic acid in acetonitrile. Gradient: 0–1 min, 100% A; 1–9 min, linear to 5% A; 9–13 min, hold; 13–17 min, re-equilibrate. Data were acquired on an Orbitrap Exploris 240 (Thermo Fisher Scientific) in polarity switching mode (70–1,050 m/z for positive; 100–2,000 m/z for negative), resolution 120,000 (MSi) and 30,000 (MS2).
"],"publication":["Multi-Omics profiling reveals immunometabolic adaptations underlying disease resilience in indigenous Lueyang Silky Fowl compared to White Leghorns."],"submitter_name":["Shuang Liu"],"submitter_affiliation":["Shaanxi University of Technology"],"organism_part":["breast"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Please update this protocol descripMuscle tissue (~50 mg) was extracted in 400 µL cold methanol:acetonitrile (1:1, v/v) with 10 µM internal standards. Samples were vortexed, sonicated on ice (30 min), and incubated at –20 °C for 1 h to precipitate proteins. After centrifugation (12,000 g, 10 min, 4 °C), supernatants were dried under vacuum and reconstituted in 200 µL 50% acetonitrile.tion
"],"organism":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14590"],"author":["Shuang Liu. Shaanxi University of Technology. 13572623262@163.com.","Abdurrahman Usman.","Murtala Isah.","Xiaoying Zhang. Shaanxi University of Technology. zhang@bio.uminho.pt."],"data_transformation_protocol":["Raw data were processed using Compound Discoverer 3.3 (Thermo Fisher Scientific) for peak picking, retention time alignment, and normalization using Progenesis QI (Waters Corporation, Milford, MA). Multivariate analyses (Principal component analysis (PCA), OPLS DA) and differential metabolite identification (VIP > 1, log2FC ≥ 0.585, FDR < 0.05) were performed in the R environment using the ropls package (Bioconductor open-source project) (https://www.bioconductor.org/packages/release/bioc/vignettes/ropls/inst/doc/ropls-vignette.html the-ropls-package). Metabolites with FC (LSF/WLC) ≥ 1.5 and an adjusted p < 0.05 were classified as significantly upregulated in the LSF group.
"],"study_factor":["Genotype"],"submitter_email":["13572623262@163.com"],"sample_collection_protocol":["Three month old, female LSF chicken and WLC (n = 3, each) were sourced from Hanzhong Agricultural Market (Shaanxi Province, China). Birds were fasted 12 h and euthanized by intraperitoneal injection of sodium pentobarbital (100 mg/kg). Breast muscle (pectoralis major) was excised, rinsed in ice cold PBS, and cut into 2 × 2 × 0.5 cm pieces. Tissue was snap frozen in liquid nitrogen and stored at –80 °C
"],"omics_type":["Metabolomics"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","Metabolomics","Multi-omics study","Thermo Scientific Dionex UltiMate HPLC system","untargeted analysis","Thermo Scientific Q Exactive HF-X","experimental blank","breast","Gallus gallus"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","Metabolomics","Multi-omics study","Thermo Scientific Dionex UltiMate HPLC system","untargeted analysis","Thermo Scientific Q Exactive HF-X","experimental blank","breast","Gallus gallus"],"mass_spectrometry_protocol":["Metabolites were separated on a Vanquish Ultra-performance liquid chromatography (UPLC; Thermo Fisher Scientific, Waltham, MA, USA) with a Waters Acquity UPLC HSS T3 column (100 × 2.1 mm, 1.8 µm) at 0.3 mL/min, 40 °C. Mobile phases A = 0.1% formic acid in water and B = 0.1% formic acid in acetonitrile. Gradient: 0–1 min, 100% A; 1–9 min, linear to 5% A; 9–13 min, hold; 13–17 min, re-equilibrate. Data were acquired on an Orbitrap Exploris 240 (Thermo Fisher Scientific) in polarity switching mode (70–1,050 m/z for positive; 100–2,000 m/z for negative), resolution 120,000 (MSi) and 30,000 (MS2).
"],"metabolite_name":["Janthitrem C","Ala-Val","Val Asp His","Butyryl trihexyl citrate","cis-Parinaric acid","MG(i-15:0/0:0/0:0)","bisorganyltrisulfane","Threoninyl-Phenylalanine","4-Guanidinobutyric acid","2-(beta-D-Mannopyranosyl)-L-tryptophan","Isobutyryl carnitine","Netilmicin","LysoPC(0:0/18:2(9Z,12Z))","Glycine, L-g-glutamyl-L-cysteinyl-, 3-methyl ester","Polidocanol","6-[5]-ladderane-1-hexanol","Tetrahydrothiophene-2-Carboxylic Acid","N-Acetylcarnosine","4'-Hydroxynomifensine","huperzine b","myrcene","Daunosamine","Niacin","(R)C(R)S-S-Propylcysteine sulfoxide","Lauroylcarnitine","4-amino-4-deoxychorismate","Amphetamine","Lys Lys Val Lys","2-Methylbutyroylcarnitine","L-Monomenthyl glutarate","Cimiracemoside D","Ser Phe","Pridinol","Thiazole","5-Hydroxyindoleacetic acid","Avocadyne Acetate","Furfural","cyclohexylammonium","Cyclohexylamine","Cinnamic acid","N1-(5-Phospho-D-ribosyl)-AMP","Carnosine","Arginine","Icosa-5,8,11,14-tetraene","Linoleamide","12,13-Epoxy-9,15-octadecadienoic acid","Mevalonolactone","O-Succinylcarnitine","Glutathione","Dopamine","Phenylalanine","Pyridoxal-5-phosphate","L-phenylalanyl-L-proline","2-Hydroxydecanoylcarnitine","Solutol HS 15","1-(3-Hydroxy-2,2,6-trimethyl-3,4-dihydrochromen-4-yl)pyrrolidin-2-one","1,2-Cyclohexanedicarboxylic acid, 4-methyl-","N-Acetyl-L-Histidine","S-Adenosyl-methionine","Proline betaine","Oleamide","Histidylalanine","Asn Ser Val Phe","Dimetacrine","Vidarabine","Indolelactic acid","12-Hydroxyheptadeca-5,8,10-trienoic acid","NEPSILON,NEPSILON,NEPSILON-TRIMETHYLLYSINE","Norleucine","Guanosine","Atraton","1-Palmitoylphosphatidylcholine","Thr Ser Leu","Inosinic acid","LysoPC(18:1(11Z))","Angenomalin","1alpha,24-Dihydroxycholecalciferol","Monoisobutyl phthalate","Buddledin A","Cyclohexanamine","Alpha-Linolenic acid","Tyrosine","Cysteinyl-Isoleucine","Phthalic acid","columbianetin","beta-Nicotinamide adenine dinucleotide","Irigenin, dibenzyl ether","Propyl 2,4-decadienoate","alpha-Eleostearic acid","Asparaginyl-Valine","Hypoxanthine","Leucomalachite green","3-(2-Hydroxyethyl)histidine","9-F1-phytoprostane","Delmopinol","Proline","D-Pipecolic acid","16-B1-phytoprostane","Diosmin","(25S)-1alpha,25,26-Trihydroxyvitamin D3/(25S)-1alpha,25S,26-trihydroxycholecalciferol","epsilon-Maleimido-lysine","beta-Alaninamide","Penicilloic acid","N-Dodecylsarcosinate","Glu Gly Thr Leu","Oxindole","Deoxyphomalone","Adenosine","Glutamylphenylalanine (isomer of 1503)","Monoethyl phthalate","Ala Tyr","L-Valine, N-(2-hydroxy-3-butenyl)-","Norhydromorphone","9-OxoODE","3-(4-Carboxybenzylidene)camphor","Octaethyleneglycol monododecyl ether","Thiram","N2-Acetyl-L-ornithine","L-(-)-Proline","LysoPA(22:4(7Z,10Z,13Z,16Z)/0:0)","LysoPC(0:0/20:4(5Z,8Z,11Z,14Z))","2-Hydroxycinnamic acid","DEET","Riboflavin lumichrome","ADP Ribose","Doxycycline","N-Palmitoyl Cysteine","7-Hydroxycoumarin","Inosine","15-Hydroxy-5,8,11,13-eicosatetraenoic acid","Ile Val Glu His","6-Hydroxy-3,4-dihydro-2(1H)-quinolinone","2-Pyrrolidinone","Ala-Leu","p-Hydroxyl-ethotoin","Alanyltryptophan","LysoPA(20:4(8Z,11Z,14Z,17Z)/0:0)","Glycylproline","oleoyl","Histidine","4-(3-Pyridyl)-3-butenoic acid","Diphenidine","Anserine","Bisnortilidin","Triethylamine","LPC 18:2","13-Hydroxyoctadecanoylcarnitine","3-Methylhistidine","2,5-Dimethylbenzaldehyde","Dodecylheptaglycol","Caffeine","Fukinanolide","gamma-Glutamylleucine","N-alpha-methylhistamine","D-Mannose 6-phosphate","Methamphetamine","REMACEMIDE","Methenamine","Ser Ser Leu","Propionylcarnitine","N,N-dimethyl-Safingol","Decanoyl-L-carnitine","Cholylhistidine","Indole-3-carboxyaldehyde","Quercetin","Adenosine-3-monophosphate","5'-Guanylic acid","Nicotinamide","Prostaglandin F2alpha methyl ester","Androstane-3,7,17-triol","7-Hydroxyoctanoylcarnitine","S-Adenosyl-L-homocysteine","Diethyl phthalate","Prostavasin","2-Hydroxy-4-[(1R)-1-hydroxy-8-methyl-6-oxononyl]-3-methyl-2H-furan-5-one","Glutamic acid","9-Hydroxydecanoylcarnitine","(E)-2-Butenyl-4-methyl-threonine","5'-Methylthioadenosine","Hept-4-enedioylcarnitine","PC(20:3(6,8,11)-OH(5)/2:0)","Gly Trp","LysoPC(0:0/18:1(9Z))","Sec-Butylpropylacetamide","5-Megastigmene-3,9-diol","Pro Phe Ser","N-(p-Toluenesulfonyl)-L-phenylalanine","N-Acetyl-3-methylhistidine","Cocamidoprpyl Betaine","Retinamide","S-Hydroxymethylglutathione","C17 Sphinganine","6-Demethylgriseofulvin","Triphenylphosphine oxid","Tris(1-chloro-2-propyl)phosphate","C16 Sphinganine","4-Aminocatechol","Val Phe","Valine","Choline","7-Oxodehydroabietic acid","Acetylcholine","D-Pantothenic acid","N-Stearoyl Arginine","Mirogabalin","Dioctyl Phthalate","Ala Phe","Dibutyl phthalate","12-amino-dodecanoic acid","Inosine 5'-monophosphate (IMP)","Benzophenone","Eicosanoyl-EA","tauroursodeoxycholic acid","Betaine","L-5-Oxoproline","L-3-Methylhistidine","Indole-3-carboxaldehyde","Glutathione (reduced)","9,12-Octadecadiynoic Acid","inosine pyruvate","5-Aminovaleric acid betaine","N,N-Dimethyldodecylamine N-oxide","3-Amino-4-methylpentanoic acid","N,N'-Dicyclohexylurea","MG(18:3(6Z,9Z,12Z)/0:0/0:0)","Benzaldehyde","Erucamide","Palmitoylcarnitine","LysoPA(22:5(7Z,10Z,13Z,16Z,19Z)/0:0)","Cytidine","Alanyllysine","Phenylalanyl-prolyl-arginine","Ribavirin monophosphate","3-hydroxydodecanoyl carnitine","Thr Val Phe","15-Methylpalmitate","Oxypurinol","Eudesmine","3-hydroxyoctanoyl carnitine","n-octyl-beta-D-thioglucopyranoside","Mdpbp","Tiagabine","p-Hydroxybenzaldehyde","Glu Ile","Sphinganine","Piperidine","P,P-Dioctyldiphenylamine","4-Pyrimidine Methanamine (hydrochloride)","(+)-Prosopinine","1-(2-Hydroxyethoxy)methyl-5-methyluracil","O-Arachidonoyl Glycidol","13,16,19-Docosatrienoic acid","Aminopentol","Asp Val Phe","Glycerylphosphorylcholine","Lauryl diethanolamide","Phosphocholine","Codeine","LysoPA(20:3(8Z,11Z,14Z)/0:0)","Etonogestrel","Deoxycholylarginine","S-Lactoylglutathione","3-Amino-2-methoxynonadec-5-en-4-ol","4-Chlorophenyl","Ser Thr Ile","Farnesyl acetone","Daidzein","22-Hydroxydocosanoic acid","N-Cyclohexyl-2-benzothiazol-amine","chenodeoxycholic acid","N-epsilon-Acetyllysine"],"additional_accession":[]},"is_claimable":false,"name":"Multi-Omics profiling reveals immunometabolic adaptations underlying disease resilience in indigenous Lueyang Silky Fowl compared to White Leghorns","description":"Sustainable avian production demands genetic strategies beyond vaccines to enhance disease resilience, particularly in indigenous breeds like Lueyang Silky Fowl (LSF), which show superior resistance compared to commercial White Leghorn chickens (WLC) but lack molecular characterization. We hypothesized LSF breast muscle harbors integrated immune–metabolic adaptations absent in WLC, reflecting evolutionary divergences and physiological ecology. We performed RNA-seq, LC-MS/MS proteomics and untargeted metabolomics on sex- and age-matched LSF and WLC breast muscle (n=3/group). Differentially expressed genes (DEGs), proteins (DAPs), and metabolites (DAMs) were identified and integrated via pathway enrichment and network analyses. LSF muscle showed 2,577 DEGs (949 up, 1,628 down), 262 DAPs (48 up, 214 down), and 197 DAMs (52 up, 145 down). Concordant enrichments spanned mitochondrial oxidative phosphorylation; amino-acid metabolism (arginine/proline; alanine/aspartate/glutamate); MAPK and calcium signaling; and antioxidant pathways (notably glutathione). Integrated networks revealed 66 shared KEGG pathways, including convergent hubs in calcium/MAPK signaling, apelin, and focal adhesion, nominating candidate markers like NOS1, GOT1, PRKCA, MAP2K6, and ATP6V1E1. These bulk-tissue signatures likely integrate myocyte-intrinsic, stromal, and resident immune-cell programs; thus, offering testable signatures for avian immunometabolic resilience. We propose validation through single-cell/spatial transcriptomics, immunohistochemistry, targeted LC-MS and metabolomics, and pathogen challenge assays. This study advances ornithological understanding by revealing breed-specific physiological adaptations in poultry, positioning muscle as proxy for systemic resilience, and providing biomarkers for genomic selection to conserve and enhance genetic diversity in resilient avian lines under intensive farming pressure.","dates":{"publication":"2026-05-27","submission":"2026-05-27"},"accession":"MTBLS14590","cross_references":{}}