GSM6602790: D7; Homo sapiens; RNA-Seq
Biospecimens were provided by the University of Miami Brain Endowment Bank™, an IRB-approved biorepository that holds frozen brain tissue annotated with demographic information and clinical variables. Postmortem brain specimens were obtained from unaffected control subjects and from cocaine-related deaths that came to routine autopsy. Medicolegal investigations and certifications of the cocaine intoxication deaths were conducted by forensic pathologists to determine the cause and manner of death. The circumstances of death and blood and brain toxicology were reviewed to identify sudden deaths due to the toxic effects of chronic cocaine abuse in persons who met the criteria for cocaine use disorder (n = 25). Drug-free age-matched control subjects (n = 20) were selected from homicides, accidental or natural deaths that had negative urine screens for all common drugs in decedents with no history of licit or illicit drug use before death. The brain samples were matched for sex (male), age, race, smoking history, PMI and brain pH to normalize factors that can affect sample quality. This study used male samples only because of the preponderance of males in the available brain bank. Cocaine use still predominates in males overall and the incidence of cocaine intoxication deaths follows this pattern. Also, the rates of polydrug abuse and psychiatric comorbidity are higher among females, further excluding females based on the criteria for subject inclusion for the present study. To isolate RNA from the samples in Trizol LS, we used the Zymo Directzol RNA miniprep kit (Zymo Research; R2050). We performed DNase treatment on all samples to ensure the removal of genomic DNA before proceeding with library preparation. RNA was analyzed for size distribution and quantity using Bioanalyzer 2000 (Agilent Technologies, USA). We used the Takara SMARTer Stranded Total RNA-seq library preparation kit to create indexed libraries from ribo-depleted RNA from each sample for sequencing (Takara; 634839). All libraries were generated simultaneously using a multiplexed library preparation strategy to ensure no variation in processing due to batch effects. Resulting libraries were analyzed for size distribution and quantity using the Agilent Bioanalyzer and Tape Station (Life Technologies) prior to sequencing.  