title: PFC expression data from germ-free vs non-germ-free, male & female mice. Measurements at day 2, 8, 14, 21.
design: PFC expression data from germ-free vs non-germ-free, male & female mice. Measurements at day 2, 8, 14, 21.
library_name: Sample 29_p
library_construction_protocol: 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. 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.  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).  Library preparation was performed by Azenta. Poly(A) enriched, strand specific.  
identifiers.namespace: European Bioinformatics Institute
identifiers.id: E-MTAB-16319:Sample 29_p