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| Status |
Public on Apr 16, 2024 |
| Title |
Heavy-10209 VTA Expression 30 Day Abstinence |
| Sample type |
SRA |
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| Source name |
Brain VTA Punch
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| Organism |
Macaca mulatta |
| Characteristics |
drinking phenotype: Heavy
tissue: Brain VTA Punch
cell type: Bulk Tissue
genotype: WT
treatment: Ethanol
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| Treatment protocol |
Monkeys (17 alcohol drinkers and 11 calorically-yoked or housing controls) were trained to obtain fluids and their meals from an operant panel that replaced one of the walls of their home cage, as described previously(Grant et al., 2008; Vivian et al., 2001). Briefly, the panels had two spouts, one to each side of a 15-inch video display screen. Near each spout, the display showed a set of three stimulus lights (white, red, and green) that indicated an active session or food or fluid availability, respectively. A centrally located recessed dowel activated the fluid spouts, and an infrared finger poke activated the pellet dispenser (env-203-1000; Med Associates). Each spout was connected via Nalgene tubing to a 1 L fluid reservoir set on a digital scale (Adventurer Pro Balances AV4101C; Ohaus). Dowel pulls, finger pokes, and fluid consumption were recorded every 500 ms via a computerized system (Dell Optiplex) using custom hardware and programming using a National Instruments interface and Labview software. Schedule-induced polydipsia, as described previously(Grant et al., 2008; Vivian et al., 2001), was used to induce alcohol self-administration in daily 16 h sessions. Briefly, a 1 g banana food pellet (Research Diets) was dispensed every 300 s (fixed time, 300 s) until a water volume equivalent to 1.5 g/kg of 4% (w/v) ethanol was consumed. Following at least 30 days of water induction, 4% ethanol replaced water. In 30-day increments, each animal consumed increasing doses of 4% ethanol: 0.5 g/kg/d, 1.0 g/kg/d, then 1.5 g/kg/d. Following consumption of the programmed volume, water was immediately available, and any remaining pellets were available on a fixed-ratio 1 (FR-1) schedule after a 2 h time-out. Following completion of ethanol induction, daily 22 h open access sessions were performed, during which water and ethanol were concurrently available. Food pellets were available on a FR-1 schedule in at least three daily meals in 2 h intervals starting at the session onset. Data were downloaded, husbandry tasks were performed, food and fluids were replenished, and fresh fruit was provided each day by technicians during the 2 h break.After drinking was initiated, subjects had 12 months of open access to alcohol for 22 hours a day. 6 months into this period, an endocrine profile was collected. After 12 months of alcohol access, subjects underwent a one-month abstinence period. Following this abstinence period, subjects returned to open access alcohol exposure for three months, then underwent another one-month withdrawal period, returned to three months of open access alcohol exposure, and finally underwent one month of withdrawal at the end of which subjects were necropsied. During open access blood was collected weekly for blood ethanol concentration measurements.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nugen Universal Plus mRNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end RNA sequencing reads (150bp long) were trimmed and filtered for quality using Trimgalore v0.6.7 (Krueger et al. 2021).
Trimmed reads were quantified using Salmon(Patro et al., 2017) v1.9.0 with the Mmul10 Macaca mulatta genome.
Sample read counts were normalized using DESeq2 v1.36.0(Love et al., 2014).
Assembly: Mmul10
Supplementary files format and content: excel file containing normalized and variance stabilized counts for genome aligned with Salmon and processed using deseq
Supplementary files format and content: excel file containing raw counts for genome aligned with Salmon and processed using deseq
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| Submission date |
Oct 03, 2023 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Cody Siciliano |
| E-mail(s) |
cody.siciliano@vanderbilt.edu
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| Organization name |
Vanderbilt University
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| Department |
Pharmacology
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| Lab |
Siciliano Lab
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| Street address |
2222 Pierce Avenue, 410 Robinson Research Building
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37203 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE244557 |
Chronic alcohol drinking modulates synchrony between midbrain gene transcription and long-lasting changes in dopamine terminal and opioid function in macaques |
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| Relations |
| BioSample |
SAMN37663457 |
| SRA |
SRX21976839 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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