Single cell gene expression profiling of adult WT and ipRGC-ablated prefrontal and motor cortices
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ABSTRACT:
PROVIDER: PRJNA640673 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12057700_1.fastq.gz | Fastqsanger.gz | |||
| SRR12057700_2.fastq.gz | Fastqsanger.gz | |||
| SRR12057701_1.fastq.gz | Fastqsanger.gz | |||
| SRR12057701_2.fastq.gz | Fastqsanger.gz | |||
| SRR12057702_1.fastq.gz | Fastqsanger.gz |
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Project description:The ventromedial prefrontal cortex (vmPFC) is a part of the limbic system engaged in higher-order functions ranging from behavioral flexibility to social cognition characteristically impaired in schizophrenia and autism. Intrinsically photosensitive retinal ganglion cells (ipRGCs) are a major source of indirect input to this area by way of the recently discovered perihabenular nucleus (PHb). Here, we demonstrate that the integrity of the vmPFC is dependent on ipRGC input: Its loss in mice causes dendritic degeneration, dysregulation of genes involved in synaptic plasticity, and depressed neuronal activity in the vmPFC. These alterations are reflected in a profound inability to suppress emotional interference in behavior.
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Project description:DNA microarray-based genome-wide transcriptional profiling and gene network analyses were used to characterize the molecular underpinnings of the frontal neocortical organization in rhesus macaque, with particular focus on the differences in the functional annotation of genes in the primary motor cortex and the prefrontal association cortex. Biofunctional analysis of the differentially expressed genes showed that the list of genes selectively expressed in the primary motor cortex were enriched with genes involved in development, oligodendrocyte function, and increased energy consumption, whereas the list of genes selectively expressed in the prefrontal association cortex were enriched with genes involved in cell morphology and calcium dynamics. These functional differences in selectively expressed genes may reflect the fundamental molecular structure of each cortex.
2012-10-01 | GSE37997 | GEO
Project description:DNA microarray-based genome-wide transcriptional profiling and gene network analyses were used to characterize the molecular underpinnings of the frontal neocortical organization in rhesus macaque, with particular focus on the differences in the functional annotation of genes in the primary motor cortex and the prefrontal association cortex. Biofunctional analysis of the differentially expressed genes showed that the list of genes selectively expressed in the primary motor cortex were enriched with genes involved in development, oligodendrocyte function, and increased energy consumption, whereas the list of genes selectively expressed in the prefrontal association cortex were enriched with genes involved in cell morphology and calcium dynamics. These functional differences in selectively expressed genes may reflect the fundamental molecular structure of each cortex. Brain tissue was obtained from 4 adolescent rhesus monkeys (Macaca mulatta) aged between 2.6 and 2.7 years that had been bred in group cages without being subjected to any experimental treatment. Adequate measures were taken to minimize pain and discomfort, in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH Publication No. 80M-bM-^@M-^S23). The monkeys were perfused with 500M-bM-^@M-^S1000 ml of ice-cold saline containing heparin sodium (1000 U/ml, Novo Heparin; Leo Pharmaceutical Products, Ballerup, Denmark) through the ascending aorta within 15 min of an overdose injection of pentobarbital sodium (50 mg/kg, i.p., Somnopentyl; Kyoritsu Shoji, Tokyo, Japan). The 2 neocortical areas (M1 and A46) were identified by sulcal landmarks. We used the forelimb region of M1 for the present analysis, which is located around the superior genu of the central sulcus. A46 was obtained from both the upper and lower banks of the principal sulcus. Each area from the left hemispheres was dissected on crushed ice and immediately frozen in liquid nitrogen.
2012-10-01 | E-GEOD-37997 | biostudies-arrayexpress
Project description:Motor-related areas of neocortex are highly differentiated into several subareas from both functional and cytoarchitectural aspects in the higher primates. To assess the molecular basis of such areal specialization, we investigated the gene expression profiles of primary motor area (M1), premotor area (dorsal and ventral) (PMd and PMv) and prefrontal area (A46) in the rhesus monkey by DNA microarray method. We found that 476 genes were differentially expressed among those areas. More than half of those genes were most abundantly expressed in M1, and most genes were complementarily expressed between M1 and A46. The expression profiles of PMd and PMv were similar to each other compared to those of M1 and A46. The data will give us a fundamental basis for further analysis of structure-function relationship of the primate brain. Keywords: cerebral neocortex; rhesus monkey; primary motor area; premotor area; prefrontal area Twenty four brain tissues from 4 areas (M1, PMd, PMv and A46) of right and left hemispheres of 3 adolescent rhesus monkeys (Macaca mulatta) aged 2.6-2.7 years which had been bred in group cages without any experimental treatments. Adequate measures were taken to minimize pain and discomfort, in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH publication no. 80-23).
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Project description:Motor-related areas of neocortex are highly differentiated into several subareas from both functional and cytoarchitectural aspects in the higher primates. To assess the molecular basis of such areal specialization, we investigated the gene expression profiles of primary motor area (M1), premotor area (dorsal and ventral) (PMd and PMv) and prefrontal area (A46) in the rhesus monkey by DNA microarray method. We found that 476 genes were differentially expressed among those areas. More than half of those genes were most abundantly expressed in M1, and most genes were complementarily expressed between M1 and A46. The expression profiles of PMd and PMv were similar to each other compared to those of M1 and A46. The data will give us a fundamental basis for further analysis of structure-function relationship of the primate brain. Keywords: cerebral neocortex; rhesus monkey; primary motor area; premotor area; prefrontal area
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Project description:Purpose: We applied polyA site sequencing (Passeq) to human Huntington's disease and control motor cortex and cerebellum to test if any genes change 3′UTR isoforms abundance. Methods: 3′ sequencing was performed on 6 motor cortices from grade 1 Huntington's patient brains, 4 motor cortices from grade 2 Huntington's patient brains, and 5 motor cortices from control brains. Cerebellum samples included 9 cerebella from grade 2-3 Huntington's patient brains, and 7 cerebella from control brains. To verify HTT isoforms in mice, sequencing was performed on 5 Q140 mouse striata and 3 wild-type mouse striata. Results: We report 11% of genes from Huntington's disease patient motor cortex exhibit a change in at least one of their 3′UTR isoforms, commensurate with the 11% of genes which show different total expression in HD motor cortex versus control. In contrast, gene isoform and expression changes are minimal (<5%) in Huntington's disease cerebellum versus controls. In the motor cortex, we show isoform and gene expression differs between between grade 1 and grade 2 brains. We identify a novel isoform of huntingtin mRNA which is conserved in wild-type and Huntington's model mice. Conclusions: This is the first study characterizing widespread alterations in 3′UTR isoform abundance in Huntington's disease. Alterations in isoform abundance may affect mRNA metabolism in Huntington's disease brains.
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