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Sample GSM3034763 Query DataSets for GSM3034763
Status Public on Nov 02, 2018
Title Male_saline_73
Sample type SRA
 
Source name Male saline
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
AmpliSeqâ„¢ 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 MS 61, 62, 63, 73, 74
73-MS
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 SAMN08663423
SRA SRX3776272

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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