|
| Status |
Public on Nov 02, 2018 |
| Title |
Male_cocaine_75 |
| Sample type |
SRA |
| |
|
| Source name |
Male cocaine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: nucleus accumbens
strain: C57BL/6J
Sex: male
|
| Treatment protocol |
cocaine was administered 10 mg/kg/d on treatment days 1 and 7; and 20 mg/kg/d for days 2-6.
|
| Growth protocol |
all animals handled for 3 days before experiment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Left and right nucleus accumbens punches were extracted in Trizol and processed as per manufacturer's instructions
AmpliSeq™ Library PLUS; RNASeq samples were barcoded and all run in a single lane with 9.4 + 4.7 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MC 67, 68, 69, 75, 76
75-MC
|
| Data processing |
Base calling and quality scores using RTA 2.1.3 from NextSeq control software 1.3.0.23
Reads were aligned to mm10 using Bowtie v. 2.1.0.0 and Samools v. 0.1.19.0
Exon-exon splice junctions were identified using Tophat v. 2.0.9
Transcriptome assembly and quantification of expression was performed with Cufflinks v. 2.2.0
Differential expression analyzed using Cuffdiff v. 2.2.0, DESeq2 and Limma
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 08, 2018 |
| Last update date |
Nov 02, 2018 |
| Contact name |
Richard E Mains |
| E-mail(s) |
mains@uchc.edu
|
| Phone |
8606798894
|
| Organization name |
University of Connecticut Health Center
|
| Department |
Neuroscience
|
| Street address |
263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-3401 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE111600 |
Exploiting Mouse Models to Understand Female Hypersensitivity to Cocaine |
|
| Relations |
| BioSample |
SAMN08663418 |
| SRA |
SRX3776277 |
