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Molecular substrates for differences between layers and regions of the entorhinal cortex during postnatal development in rats

ABSTRACT: We report the first full transcriptome analysis of layer II and deep layers of the medial and lateral entorhinal cortex during postnatal development. Our analysis showed that postnatal timepoint was the most important element in entorhinal cortex transcriptional dynamics, followed by laminar differences. There were fewer differentially expressed genes between the medial and lateral parts of the entorhinal cortex, and most of these were found in layer II.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE85789 | GEO | 2017/08/01

SECONDARY ACCESSION(S): PRJNA339395

REPOSITORIES: GEO

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Project description:Specific vulnerability of neurons in the human entorhinal cortex has been associated with the onset of disease. Gene expression is analyzed to define the molecular characteristic of those neurons. Experiment Overall Design: Human tissue collection and dissection. Brain samples were collected from four individuals with no clinical evidence of neurological disease and no neuropathological evidence of neurodegeneration. Tissue samples were obtained from the neurological tissue bank (UIPA) and from the Neurological Research Tissue Bank (BTIN, Madrid). The mean postmortem interval (PMI) of the tissue was 6 h and each subject died in hospital due to either cardiac or infectious diseases. The tissue was obtained according to local ethical and legal regulations concerning the use of human post-mortem tissue for biomedical research. Frozen tissue samples were collected from the entorhinal cortex [EC; Brodmann area (BA) 28], at coronal level 27 of the Atlas of Paxinos. Tissue samples corresponded to either upper (CES), lower (CEI) or the entire EC (CET). Two adjacent vertical columns comprising the full thickness of the EC were dissected under magnification with a Leica M50 stereomicroscope. One of them was then divided into two blocks, corresponding to CES and CEI, while the remaining column was processed as CET. RNA sample preparation. Cerebral tissue was homogenised in liquid nitrogen with a pestle and mortar, and the total RNA was isolated using the RNeasy Mini Kit and QIAshredder (Qiagen). The total RNA concentration and purity were determined using an Agilent2100 Bioanalyzer (Agilent Biotechnologies, Palo, Alto, CA) and by agarose gel electrophoresis. Subsequently, cDNA was synthesized using the One-Cycle cDNA Synthesis kit (Affymetrix), according to the protocol described in the Expression Analysis Technical Manual. Biotinylated cRNA probes were generated from each cDNA sample following the IVT Labeling kit instructions (Affymetrix), and the cRNA synthesized was purified with the GeneChip Sample Cleanup Module (Affymetrix). The concentration and purity of the biotinylated cRNA was determined using an Agilent2100 Bioanalyzer (Agilent Biotechnologies, Palo, Alto, CA) and by agarose gel electrophoresis.

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Molecular substrates for differences between layers and regions of the entorhinal cortex during postnatal development in rats

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