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Integrated Multi-omics Profiling of Mouse Brain Tissue Using the AllPrep Methods versus Traditional Extraction Methods

ABSTRACT: This study systematically evaluated the AllPrep co-extraction strategy in multi-omics analysis of mouse brain tissues. At the transcriptomic level, AllPrep produced higher RNA yields and an 88.14% gene detection rate, ensuring broader coverage. In proteomics, it preserved identification depth while improving detection of membrane proteins, ubiquitin ligases, and transcription factors. Phosphoproteomics further revealed 4,347 high-confidence phosphorylation sites, including CAMK family regulatory patterns. Integrated analysis showed stronger RNA–protein correlations and enriched neuroscience-related pathways. Overall, AllPrep provides a standardized, scalable workflow that enhances data quality and supports deeper exploration of neurobiological mechanisms.

ORGANISM(S): Mus musculus

PROVIDER: GSE308738 | GEO | 2026/03/18

REPOSITORIES: GEO

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Project description:Extraction is the first and most important step in obtaining the effective ingredients of medicinal plants. Mentha longifolia (L.) L. is of considerable economic importance as a natural raw material for the food and pharmaceutical industries. Since the effect of different extraction methods (traditional and modern methods) on the quantity, quality and antimicrobial activity of the essential oil of this plant has not been done simultaneously; the present study was designed for the first time with the aim of identifying the best extraction method in terms of these features. For this purpose, extracting the essential oil of M. longifolia with the methods of hydrodistillation with Clevenger device (HDC), steam distillation with Kaiser device (SDK), simultaneous distillation with a solvent (SDE), hydrodistillation with microwave device (HDM), pretreatment of ultrasonic waves and Clevenger (U+HDC) and supercritical fluid (SF) were performed. Chemical compounds were identified by gas chromatography coupled with mass spectrometer (GC-MS). Antimicrobial activity of essential oils against various clinical microbial strains was evaluated by agar diffusion method and determination of the minimum inhibitory concentration and minimum bactericidal concentration (MIC and MBC). The results showed that the highest and lowest yields of M. longifolia leaf essential oil belonged to HDC (1.6083%) and HDM (0.3416%). The highest number of compounds belonged to SDK essential oil and was equal to 72 compounds (with a relative percentage of 87.13%) and the lowest number of compounds was related to the SF essential oil sample (7 compounds with a relative percentage of 100%). Piperitenone (25.2-41.38%), piperitenone oxide (22.02-0%), pulegone (10.81-0%) and 1,8-cineole (5-35.0%) are the dominant and main components of M. longifolia essential oil were subjected to different extraction methods. Antimicrobial activity results showed that the lowest MIC value belonged to essential oils extracted by HDM, SDK, SDE and U+HDC methods with a value of 1000 μg/mL was observed against Gram-negative bacteria Shigella dysenteriae, which was 5 times weaker than rifampin and 7 times weaker than gentamicin. Therefore, it can be concluded that in terms of efficiency of the HDC method, in terms of the percentage of compounds of the HDM method, and in terms of microbial activity, the SDK, HDM and U+HDC methods performed better.

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Integrated Multi-omics Profiling of Mouse Brain Tissue Using the AllPrep Methods versus Traditional Extraction Methods

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