Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA379499: On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome (Cortical Area 32 - A32)

来源: NCBI / GSE96731
提交时间: Mar 16 2017
释放时间: Mar 17 2017
最后更新时间: May 15 2019

概要: This is the first description of the relationship between chronic ethanol self-administration and the brain transcriptome in a non-human primate (rhesus macaque). Twenty nine male animals self-administered ethanol on a daily basis for over 12 months. Gene transcription was quantified with RNA-Seq in the cortical Area 32. We constructed coexpression and cosplicing networks, and we identified areas of preservation and areas of differentiation between regions and network types. Correlations between intake and transcription included largely distinct gene sets and annotation categories across brain regions and between expression and splicing; positive and negative correlationswere also associated with distinct annotation groups. Our cosplicing analysis further identified the genes affected only at the exon inclusion level. In the Area 32 coexpression network, we identified a distinct hub set that included Ppp3r1 and Myeov2. Overall, the data illustrate that excessive ethanol self-administration is associated with broad expression and splicing mechanisms that involve membrane and synapse genes.

项目整体设计: Thirty one samples of Rhesus Macaques that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 31, 4-11 years, 6-8 kg), were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. We then removed one outlier resulting in 30 samples presented here.

GEN 数据集:
GEND000601
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处理方案: Male rhesus monkeys that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 31, 4-11 years-old, 6-8 kg) were used. They were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. They were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session.The monkeys were from four cohorts, referred to as cohorts 4, 5, 7a and 7b in the Monkey Alcohol Tissue Research Resource (www.MATRR.com). These cohorts where selected because they all had approximately 90 days of induction followed by approximately two 6-month periods of alcohol open access. All monkeys were individually housed (quadrant cages, 0.8 m x 0.8 m x 0.9 m) in a room with controlled light cycle (11 hours lights on, 13 hours lights off), temperature (20-22oC) and humidity (65%). The monkeys had visual, auditory and olfactory contact with other monkeys. They were weighed weekly.
提取方案: Monkeys were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session. Preparation of brain tissue was described previously (Davenport et al., 2014) and the tissues were collected as part of the MATRR. Necropsy occurred at the time when they would normally begin their drinking session; monkeys were anesthetized with ketamine (10 mg/kg) and maintained on isoflurane. The brains were perfused with ice-cold oxygenated artificial cerebral spinal fluid, removed (< 5 min post-mortem) and sectioned according to each monkey’s individual MRI (Daunais et al., 2010). The prefrontal cortex was isolated, and Area 32 was dissected and frozen in liquid nitrogen.
建库方案: Library formation (TruSeq Stranded RNA-Seq with RiboZero Gold rRNA depletion) and sequencing on a HiSeq 2000 were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 4 per lane, yielding approximately 50 million total reads per sample.
测序信息
分子类型: rRNA- RNA
库的片段类型: SINGLE
库的链类型: Forward
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2000
链特异性: Specific
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数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度