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| Status |
Public on Mar 17, 2017 |
| Title |
RNA130128RH_24 |
| Sample type |
SRA |
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| Source name |
Dissected Tissue (Brain) - Cortical Area 32 (A32)
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| Organism |
Macaca mulatta |
| Characteristics |
matrr (monkey alcohol tissue research resource) id: 10089
cohort: COHORT 7a
avg age at beginning of 1.5 g/kg etoh induction: 4.18
avg age after second 6 months of open access: 5.7
Sex: Male
drinking category: LD
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| Treatment protocol |
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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
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.
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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Low Drinker: not BD, not HD, and not VHD
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| Data processing |
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
Alignment: Reads were aligned to MacaM assembly (Zimin et al., 2014) using STAR v.2.3.0e (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax=3,outFilterScoreMinOverLread=0.33,outFilterMismatchNoverLmax=0.03, outFilterMultimapNmax=1.
After removing one sample outlier from the set, upper-Quartile normalization was performed using the edgeR Bioconductor package. Genes with at least 100 average reads per sample and exons with more than 10 average reads were retained for further analysis.
Genome_build: MacaM
Supplementary_files_format_and_content: RNASeq017_exon_reads_UQNormalized_for_GEO.csv: first column has the exon ID (a combination of chromosome number, start, and end location of exon, and gene symbol). subsequent 30 columns provide the normalized reads for each sample for each exon
Supplementary_files_format_and_content: RNASeq017_gene_reads_UQNormalized_for_GEO.csv: first column has the Gene Symbol, and subsequent 30 columns provide the normalized reads for each sample for each gene
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| Submission date |
Mar 16, 2017 |
| Last update date |
May 15, 2019 |
| 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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| Platform ID |
GPL14954 |
| Series (2) |
| GSE96731 |
On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome (Cortical Area 32 - A32) |
| GSE96732 |
On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome |
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| Relations |
| BioSample |
SAMN06610093 |
| SRA |
SRX2647816 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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