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Sample GSM723281 Query DataSets for GSM723281
Status Public on May 13, 2011
Title NAc_cocaine_smallRNA
Sample type SRA
Source name Nucleus accumbens
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Brain
treatment: Cocaine
read length: 50
Treatment protocol Mice were given a saline or cocaine injection and had their locomotor activity monitored for the subsequent 45 minutes. In the experiments in which RNA from NAc lysates was used for miRNA-Seq library preparation, animals were given injections of 20 mg/kg cocaine or saline (10 ml/kg) intraperitoneally each for 7 days. For all other experiments, animals received a lower dose of cocaine (10 mg/kg) on the first and last (7th) day, with the standard 20 mg/kg cocaine dose on days 2-6.
Growth protocol All mice were allowed to acclimate to the colony for at least one week before handling or injections. Mice were kept in the University of Connecticut Health Center animal facility on a 12 h light/dark cycle (lights on 7:00 am to 7:00 pm) and handled in accordance with University of Connecticut Health Center Institutional Animal Care and Use Committee guidelines. To reduce stress from handling during the injections, animals in all groups were handled for 1min/animal/day for 2-3 days prior to the start of injections. During injections, animals were brought into the behavior room to acclimate to the new environment for 45-60 minutes each day before the beginning of experiments.
Extracted molecule total RNA
Extraction protocol TRIzol; PSD sample buffers contained RNASecure
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
Data processing Sequences were extracted from image files using Firecrest and Bustard. The 3'adaptor sequences were trimmed from the reads, and reads 18-30 nt in length were aligned to all annotated mouse microRNAs from miRBase (; version 16) with Bowtie (; version 0.12.7); only perfectly aligning reads were considered for miRNA expression level analysis. A custom Perl script was used to calculate the number of reads aligning to each specific miRNA gene.
Submission date May 12, 2011
Last update date May 15, 2019
Contact name Brenton R Graveley
Phone 860-679-2090
Organization name University of Connecticut Health Center
Department Genetics and Genome Sciences
Street address 400 Farmington Avenue
City Farmington
State/province CT
ZIP/Postal code 06030-3301
Country USA
Platform ID GPL11002
Series (1)
GSE29261 Cocaine-regulated expression of striatal microRNAs
SRA SRX062917
BioSample SAMN00618865

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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