{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/PXD080591_community_annotated.sdrf.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/Culter_alburnus_runx2b_proteome_sdrf.tsv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901872_WT3_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901878_Ho3_9.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901875_He3_6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901874_He2_5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901873_He1_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901876_Ho1_7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901870_WT1_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901877_Ho2_8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/MKJ1901871_WT2_2.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080591/20251107_224345_sp_MJ20251014053_PP20251023174.sne"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["21207054@zju.edu.cn"],"submitter":["Xiaohui Xu"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["muscle/myoseptal tissue","Culter alburnus","intermuscular bone","runx2b","Culter alburnus; intermuscular bone; runx2b; proteomics; dia; lc-ms/ms; gene editing; skeletal development; muscle/myoseptal tissue","proteomics","dia","gene editing","skeletal development","lc-ms/ms"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD080591"],"tissue":["Skeletal Muscle"],"sample_protocol":["Muscle tissues from regions associated with intermuscular bone development were collected from wild-type, heterozygous runx2b mutant, and homozygous runx2b mutant Culter alburnus individuals. Samples were rapidly dissected, snap-frozen in liquid nitrogen, and stored at -80°C until protein extraction. Total proteins were extracted from frozen tissues using lysis buffer. After tissue grinding, sonication, and centrifugation, protein concentration was determined using the BCA method, and protein quality was assessed by SDS-PAGE. Equal amounts of proteins were reduced, alkylated, digested with trypsin, desalted, and subjected to LC-MS/MS analysis."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw DIA mass spectrometry data were searched against the Culter alburnus protein database using Spectronaut software version 19. Protein identification was controlled at a false discovery rate of 1% or less. Protein abundance was quantified using the MaxLFQ method. Differentially expressed proteins were identified using thresholds of fold change greater than 1.2 or less than 0.83 and P value less than 0.05."],"omics_type":["Proteomics"],"labhead":["Jianbo Zheng"],"instrument_platform":[""],"labhead_affiliation":["Affiliation* Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China"],"submission_type":["PARTIAL"],"species":["Culter Alburnus"],"submitter_mail":["xiaohuixu71@outlook.com"],"publication":["42511132 Xu Y, Xu X, Li F, Li C, Huang C, Zheng J. Integrated Transcriptomic and Proteomic Analysis Reveals &lt;i&gt;Runx2b&lt;/i&gt;-Associated Molecular Regulation of IB Development in &lt;i&gt;Culter alburnus&lt;/i&gt;. Animals (Basel). 2026 16(14):2255 10.3390/ani16142255"],"submitter_affiliation":["Yangtze Delta Region Institute of Tsinghua University Zhejiang"],"submitter_country":["China"],"pubmed_abstract":["Intermuscular bones (IBs) are ossified structures within the myoseptal connective tissues of cyprinid fishes and negatively affect eating quality and processing suitability. Although <i>runx2b</i> has been shown to be essential for IB formation, the molecular changes associated with <i>runx2b</i>-mediated IB reduction or loss remain poorly understood. In this study, <i>runx2b</i>-edited <i>Culter alburnus</i> F1 individuals were generated and classified into wild-type, heterozygous mutant, and homozygous mutant groups. Skeletal staining revealed a clear genotype-associated phenotypic gradient, with normal IBs in wild-type individuals, markedly reduced IBs in heterozygous mutants, and complete IB absence in homozygous mutants. Integrated transcriptomic and proteomic analyses were then performed using matched muscle/myoseptal tissues to characterize molecular changes associated with this phenotypic gradient. Global mRNA-protein correlations were weak and DEG-DEP overlaps were limited, suggesting that transcriptomic changes alone cannot fully explain protein-level remodeling after <i>runx2b</i> mutation. Functional enrichment and integrated omics analysis highlighted coordinated changes in cytoskeletal organization, extracellular matrix remodeling, cell adhesion, calcium-related signaling, muscle-associated processes, and ossification-related pathways. Representative candidate molecules, including <i>MYH1s</i>, <i>CDH26</i>, <i>PLIN5</i>, <i>PAH</i>, <i>HBA</i>/<i>HBB</i>, <i>GPX4</i>, <i>KRT1</i>, <i>GSN</i>, <i>LGALS9</i>, and <i>ANXA3</i>, were mainly associated with structural, metabolic, and microenvironmental remodeling rather than being interpreted as direct downstream osteogenic targets of <i>runx2b</i>. Overall, these findings suggest that <i>runx2b</i>-associated IB reduction and loss may involve coordinated remodeling of the myoseptal osteogenic microenvironment rather than disruption of a single ossification pathway. This study provides a discovery-oriented multi-omics resource and a hypothesis-generating molecular model for future functional validation of IB development in cyprinid fishes."],"pubmed_title":["Integrated Transcriptomic and Proteomic Analysis Reveals &lt;i&gt;Runx2b&lt;/i&gt;-Associated Molecular Regulation of IB Development in &lt;i&gt;Culter alburnus&lt;/i&gt;."],"pubmed_authors":["Xu Yi Y, Xu Xiaohui X, Li Fei F, Li Caiyan C, Huang Cancan C, Zheng Jianbo J"],"additional_accession":[]},"is_claimable":false,"name":"Integrated transcriptomic and proteomic analysis reveals Runx2b-associated molecular regulation of intermuscular bone development in Culter alburnus","description":"This dataset contains LC-MS/MS-based proteomic data generated from muscle/myoseptal tissues of wild-type, heterozygous runx2b mutant, and homozygous runx2b mutant Culter alburnus individuals. The study aimed to characterize proteomic changes associated with runx2b-mediated intermuscular bone reduction and loss. Three biological replicates were analyzed for each genotype group. Differential protein abundance analysis and integrated transcriptomic-proteomic analysis were used to identify candidate proteins and functional modules associated with extracellular matrix remodeling, cytoskeletal organization, calcium signaling, muscle contraction, and osteogenic regulation during intermuscular bone 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