{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thomaz Bastiaanssen"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16319"],"description":["Maturation of the gut microbiota coincides with neurodevelopmental processes such as myelination, essential for efficient neural signal transmission. While its role in adult prefrontal cortex (PFC) myelination is known, effects on early-life myelin formation, growth, and integrity remain unclear.   Here, we track gene expression in the PFC of germ-free (GF) and non-germ-free (conventional) mice.  Alongside metabolomics (HP/LC) from the same region across early life development, in males and females.   Metabolomics data available here <URL PLACEHOLDER>  In GF mice, we observed sex- and age-dependent alterations in pathways linked to neuronal activity and myelination, with myelin-related transcriptomic changes correlating with functional shifts in neurotransmission- and metabolism-related metabolites over time. Myelin growth and integrity were also affected in a sex- and time-dependent manner. As microglia regulate neuronal activity and engulf myelin, we examined microbiota-microglia interactions and found altered expression of genes involved in microglia maturation and synaptic pruning in both species. In zebrafish larvae, the microbiota influenced the spatial distribution of microglia and oligodendrocytes within the brain and spinal cord. These findings reveal conserved microbiota-mediated modulation of neuronal activity, myelination, and glial maturation in early life, providing a foundation for future studies into these mechanisms. These files contain the RNAseq data underlying this study."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Library preparation was performed by Azenta. Poly(A) enriched, strand specific.","Nucleic Acid Extraction - RNA was extracted from the PFC using the RNeasy Plus Universal Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quality and concentrations were then measured using a Nanodrop ND-1000 (Thermo Scientific).","Sequencing - Strand-Specific mRNA sequencing was conducted by Azenta) on the Illumina NovaSeq 6000 (S4 flow cell, 2x 150bp Pair-End (PE) configuration)","Sample Collection - Mice designated for fresh culls were sacrificed by decapitation between 10 am and 12 pm. Brain regions were rapidly dissected on ice. Crude isolation of the whole PFC and surrounding cortical regions was performed by first removing the olfactory bulbs. Briefly, a coronal cut was made at the anterior extent of the brain to define the dissection boundary (approx. Bregma 2.93-1.69 mm) The ventral portion of this section (olfactory bulb, nucleus accumbens, piriform cortex, and other subcortical regions), was carefully discarded. The remaining dorsal cortical tissue, encompassing the prefrontal cortex, orbital cortex, and adjacent cortical areas, was isolated for subsequent analyses. This approach aimed to capture a broad region of the prefrontal cortex relevant to our study while minimizing contamination from ventral and subcortical structures. Notably, this would have included both grey and white matter tissue. All biological samples were promptly snap-frozen on dry ice and stored at -80°C until further analysis."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Quality of sequences was assessed with using FastQC v.0.11.8 Reads were aligned to mouse genome: GRCm39[63] using STAR 2.7.10a and sequence reads overlapping genes were counted using HTSeq 2.0.3","Data Transformation - Sequence reads overlapping genes were counted using HTSeq 2.0.3"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Thomaz Bastiaanssen"],"additional_accession":[]},"is_claimable":false,"name":"PFC expression data from germ-free vs non-germ-free, male & female mice. Measurements at day 2, 8, 14, 21.","description":"Maturation of the gut microbiota coincides with neurodevelopmental processes such as myelination, essential for efficient neural signal transmission. While its role in adult prefrontal cortex (PFC) myelination is known, effects on early-life myelin formation, growth, and integrity remain unclear.   Here, we track gene expression in the PFC of germ-free (GF) and non-germ-free (conventional) mice.  Alongside metabolomics (HP/LC) from the same region across early life development, in males and females.   Metabolomics data available here <URL PLACEHOLDER>  In GF mice, we observed sex- and age-dependent alterations in pathways linked to neuronal activity and myelination, with myelin-related transcriptomic changes correlating with functional shifts in neurotransmission- and metabolism-related metabolites over time. Myelin growth and integrity were also affected in a sex- and time-dependent manner. As microglia regulate neuronal activity and engulf myelin, we examined microbiota-microglia interactions and found altered expression of genes involved in microglia maturation and synaptic pruning in both species. In zebrafish larvae, the microbiota influenced the spatial distribution of microglia and oligodendrocytes within the brain and spinal cord. These findings reveal conserved microbiota-mediated modulation of neuronal activity, myelination, and glial maturation in early life, providing a foundation for future studies into these mechanisms. These files contain the RNAseq data underlying this study.","dates":{"release":"2025-12-20T00:00:00Z","modification":"2026-05-27T17:32:57.364Z","creation":"2025-11-28T14:52:50.302Z"},"accession":"E-MTAB-16319","cross_references":{"ENA":["ERP185801"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}