RNAseq data from: Medial prefrontal cortex samples of glutamate dehydrogenase-deficient mice, stress-exposed or -naive, and their Nestin-Cre+ controls
Data files
Jun 21, 2023 version files 212.33 GB
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225_S5_R1_001.fastq
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257_S6_R1_001.fastq
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310_S10_R1_001.fastq
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313_S11_R1_001.fastq
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320_S12_R1_001.fastq
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413_S7_R1_001.fastq
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414_S8_R1_001.fastq
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432_S1_R1_001.fastq
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455_S9_R1_001.fastq
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560_S2_R1_001.fastq
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635_S3_R1_001.fastq
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638_S4_R1_001.fastq
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README.md
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Sample_683.fastq
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Sample_688.fastq
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Sample_689.fastq
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Sample_730.fastq
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Sample_739.fastq
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Sample_782.fastq
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Sample_786.fastq
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Sample_787.fastq
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Sample_793.fastq
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Sample_795.fastq
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Sample_820.fastq
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Sample_821.fastq
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Sample_869.fastq
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Sample_871.fastq
Abstract
Glutamate abnormalities in the medial prefrontal cortex (mPFC) are associated with cognitive deficits. We previously showed that homozygous deletion of CNS glutamate dehydrogenase 1 (Glud1), a metabolic enzyme critical for glutamate metabolism, leads to schizophrenia-like behavioral abnormalities and increased mPFC glutamate; mice heterozygous for CNS Glud1 deletion (C-Glud1+/- mice) showed no cognitive or molecular abnormalities. Here, we examined the protracted behavioral and molecular effects of mild injection stress on C-Glud1+/- mice. We found spatial and reversal learning deficits, as well as large-scale mPFC transcriptional changes in pathways associated with glutamate and GABA signaling, in stress-exposed C-Glud1+/- mice, but not in their stress-naïve or C-Glud1+/+ littermates. Interestingly, these effects were observed several weeks following stress exposure, and the expression levels of specific glutamatergic and GABAergic genes differentiated between high and low reversal learning performance. An increase in MiR203-5p expression immediately following stress may provide a translational regulatory mechanism to account for the delayed effect of stress exposure on cognitive function. Our findings show that chronic glutamate abnormalities interact with acute stress to induce cognitive deficits, and resonate with gene x environment theories of schizophrenia. Stress-exposed C-Glud1+/- mice may model a schizophrenia high-risk population, which is uniquely sensitive to stress-related ‘trigger’ events.
Methods
RNA was extracted from 28 mPFC samples (n=5-9 per group, approximately equal numbers of males and females) as previously described20,90, and sent to the Technion Genome Center for genome-wide RNA sequencing (RNA-seq) and bioinformatical analysis. The experiment was comprised of two batches; the first included samples from three of the four groups (C-Cre+/Control, C-Cre+/Stress and C-Glud1+/-/Stress), and the second included new samples from the three aforementioned groups, and added the forth group (C-Glud1+/-/Control). Findings from both batches were combined, taking into account batch and sex effects. RNA was prepared using the SMARTer Stranded Total RNA-Seq Kit v2 – Pico preparation kit according to the manufacturer’s instructions. RNA-seq library preparation, sequencing (using the Illumina HiSeq 2500 sequencer for first batch; Illumina NextSeq 550 for the second), and data analysis was performed by the Technion Genome Center. The quality of the libraries was evaluated using FASTQC (v 0.11.5), quality and adapter trimming was conducted via trim galore (uses cutadapt v 1.10), and mapping was conducted via Tophat2 v 2.1.0, (uses short read aligner Bowtie2 v 2.2.6). At the end of this process, the total reads after trimming ranged between 35-46 million reads per sample. Gene counting was conducted via HTseq-count (v0.6.1). Due to the ribosomal depletion process in the library preparation protocol and the expected ribosomal sequence reads, counting was performed with a modified annotation file which includes the 45s ribosome annotation for better accuracy. Only counted reads without 45s were used for the subsequent analysis. Uniquely mapped reads, aligned with high confidence to a single genomic location, ranged between 25-38 million reads per sample. Differential gene expression was performed by DESeq2 (v1.28.1).
Usage notes
Application and version used: FASTQC (v 0.11.5)