|
| Status |
Public on May 13, 2011 |
| Title |
PSD_cocaine_smallRNA |
| Sample type |
SRA |
| |
|
| Source name |
Striatal postsynaptic density
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Brain
treatment: Cocaine
read length: 40
|
| 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 (www.mirbase.org; version 16) with Bowtie (bowtie-bio.sourceforge.net; 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 |
| E-mail(s) |
graveley@uchc.edu
|
| 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 |
|
| Relations |
| SRA |
SRX062919 |
| BioSample |
SAMN00618867 |
