Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA803898 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [HiC]
| PRJNA803901 | ENA
Project description:Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [RNA-seq]
| PRJNA803900 | ENA
Project description:Purpose:The goals of this study are to investigate the 3D chromatin architecture of cortical neurons in rhesus monkeys treated with morphine for 90 days using digestion-ligation-only high-throughput chromosome conformation capture technology combined with transcriptome profiling (RNA-seq).
2023-09-12 | GSE196209 | GEO
Project description:Purpose: The goals of this study are to investigate the 3D chromatin architecture of cortical neurons in rhesus monkeys treated with morphine for 90 days using digestion-ligation-only high-throughput chromosome conformation capture technology combined with transcriptome profiling (RNA-seq).
2023-09-12 | GSE196210 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-09-12 | GSE196212 | GEO
Project description:The expression of linear DNA sequence is precisely regulated by the three-dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neurons is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology to investigate the effects of morphine on the 3D chromatin architecture of primate cortical neurons. After receiving continuous morphine administration for 90 days on rhesus monkeys, we discovered that morphine re-arranged chromosome territories, with a total of 391 segmented compartments being switched. Morphine altered over half of the detected topologically associated domains (TADs), most of which exhibited a variety of shifts, followed by separating and fusing types. Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops. Moreover, all identified differentially expressed genes from the RNA sequencing data were mapped to the specific TAD boundaries or differential loops, and were further validated for changed expression. Collectively, an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated with morphine effects. Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
| S-EPMC10787020 | biostudies-literature
Project description:m6a modifications following morphine exposure or Alkbh5 siRNA in primary cortical neuron cultures
| PRJNA1019381 | ENA
Project description:m6a modified RNA and unmodified RNA were quantified in primary neuronal cultures following either siRNA knockdown of Alkbh5 or chronic morphine exposure for 3 days. The goal was to identify mRNA that have m6A modifications following one or more treatment conditions.
2024-09-01 | GSE243685 | GEO
Project description:Genome-wide transcriptional profiling allows characterization of the molecular underpinnings of neocortical organization, including cortical areal specialization, laminar cell type diversity and functional anatomy. Microarray analysis of individual cortical layers across sensorimotor and association cortices in rhesus macaque demonstrated robust and specific laminar and areal molecular signatures driven by differential expression of genes associated with specialized neuronal function. Gene expression corresponding with laminar architecture was generally similar across cortical areas, although genes with robust areal patterning were often highly laminar as well, and these patterns were more highly conserved between macaque and human as compared to mouse. Layer 4 of primate primary visual cortex displayed a distinct molecular signature compared to other cortical regions, a specialization not observed in mouse. Overall, transcriptome-based relationships were strongest between proximal layers in a cortical area, and between neighboring areas along the rostrocaudal axis, reflecting in vivo cortical spatial topography and therefore a developmental imprint.
2012-03-21 | GSE31613 | GEO
Project description:Genome-wide transcriptional profiling allows characterization of the molecular underpinnings of neocortical organization, including cortical areal specialization, laminar cell type diversity and functional anatomy. Microarray analysis of individual cortical layers across sensorimotor and association cortices in rhesus macaque demonstrated robust and specific laminar and areal molecular signatures driven by differential expression of genes associated with specialized neuronal function. Gene expression corresponding with laminar architecture was generally similar across cortical areas, although genes with robust areal patterning were often highly laminar as well, and these patterns were more highly conserved between macaque and human as compared to mouse. Layer 4 of primate primary visual cortex displayed a distinct molecular signature compared to other cortical regions, a specialization not observed in mouse. Overall, transcriptome-based relationships were strongest between proximal layers in a cortical area, and between neighboring areas along the rostrocaudal axis, reflecting in vivo cortical spatial topography and therefore a developmental imprint. Tissue from male and female monkeys (n = 2-3 animals/gender) was collected from anterior cingulate gyrus (ACG), layers 2, 3, 5, 6; orbitofrontal cortex (OFC), layers 2, 3, 5, 6; dorsolateral prefrontal cortex (DLPFC), layers 2-6; primary motor cortex (M1), layers 2, 3, 5, 6; primary somatosensory cortex (S1), layers 2-6; primary auditory cortex (A1), layers 2-6; primary visual cortex (V1), layers 2-6 including 4A, 4B, 4Calpha (4Ca), 4Cbeta (4Cb); secondary visual cortex (V2), layers 2-6; middle temporal area (MT), layers 2-6; temporal area (TE), layers 2-6; hippocampus, CA1, CA2, CA3, dentate gyrus (DG); and dorsal lateral geniculate nucleus (LGN), magnocellular, parvocellular and koniocellular divisions. Due to the limited number of samples that could be amplified concurrently, amplifications were performed in 3 batches (batches A-C, containing 102, 119 and 10 experimental samples, respectively). To control for batch effects, common RNA pool control samples were amplified and hybridized in each batch. These included LCM extracted hippocampus CA3 samples from the current study and a whole rhesus brain RNA pool (Biochain). These control samples were hybridized in 6 replicates in batch A and B and in 3 replicates in batch C (3 replicates per 96 well plate).
2012-03-21 | E-GEOD-31613 | biostudies-arrayexpress