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| Status |
Public on Feb 06, 2020 |
| Title |
Effect of Chronic Ethanol Consumption in Rhesus Macaques on the Nucleus Accumbens Core Transcriptome |
| Organism |
Macaca mulatta |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The current study was undertaken to expand on observations that transcriptome changes identified in the NAcc of Rhesus macaques underlies excessive ethanol consumption. Genome-wide RNA-Seq was used to examine the NAcc transcriptome in control, low/binge drinking and heavy/very heavy drinking animals. One key goal of the study was to determine if, as predicted and suggested by the epigenetic studies, excessive chronic ethanol consumption involves genes enriched in annotations associated with synaptic plasticity and specifically glutamate and GABA signaling plasticity.
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| Overall design |
NAcc samples were obtained from four cohorts (cohorts 4, 5, 7a and 7b) of unrelated adult, male rhesus macaques (Macaca mulatta).Monkeys were trained to use operant drinking panels to obtain all fluids (water and/or ethanol) and meals. Once trained, they underwent four months of schedule-induced polydipsia (SIP) to induce ethanol self-administration in daily sessions (Grant et al., 2008). Control subjects were housed in the same room as the ethanol drinking subjects of the same cohort and participated in all experimental manipulations. For the controls, SIP and self-administration conditions were identical, with the exception that both spouts dispensed water. Libraries without strand orientation were prepared using the TruSeq RNA Sample Preparation Kit version 2 (Illumina). Libraries were sequenced according to specification on a HiSeq 2500 (Illumina) at the Oregon Health and Science University Massively Parallel Sequencing Shared Resource. PolyA-selected libraries were multiplexed three per lane, yielding an average of 76 million total single-end reads per sample. FastQC (Babraham Bioinformatics) was used for quality checks on the raw sequence data. Reads were aligned to MacaM genome assembly using STAR version 2.5.2b (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax = 2 and outFilterMultimapNmax = 1. Using HTSeq version 0.6.1p1 (Anders et al., 2015) and the MacaM_Rhesus_Genome_Annotation_v7.8.1 GTF annotation file read counts were summarized at the gene level. On average, 70% of reads uniquely mapped to the MacaM genome. Generalized linear models, using DESeq2 (Love et al., 2014), were used to detect differential expression between High Drinkers and Controls (HDvsControls), Low Drinkers and Controls (LDvsControl), and High Drinkers and Low Drinkers (HDvsLD).
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| Contributor(s) |
Walter N, Hitzemann R, Grant K, Zheng C, Cervera-Juanes R, Cuzon-Carlson V, Darakjian P, Lockwood D, Searles R |
| Citation(s) |
33942443 |
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| Submission date |
Feb 05, 2020 |
| Last update date |
Nov 17, 2021 |
| Contact name |
Priscila Darakjian |
| E-mail(s) |
darakjia@ohsu.edu
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| Organization name |
Oregon Health and Science University
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| Department |
Behavioral Neuroscience
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| Street address |
3181 SW Sam Jackson Park Road, L470
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platforms (1) |
| GPL19129 |
Illumina HiSeq 2500 (Macaca mulatta) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA604902 |
| SRA |
SRP247304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144783_RhesusNaCore_NormalizedCounts_DESeq2.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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