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Sample GSM1062208 Query DataSets for GSM1062208
Status Public on Jan 10, 2013
Title NAc_saline_rep1
Sample type SRA
Source name Nucleus accumbens
Organism Mus musculus
Characteristics tissue: Nucleus accumbens
strain: C57BL/6
treatment: Saline
Treatment protocol Animals were given Saline (10 ml/kg/day) or Cocaine (10 or 20mg/kg/day) intraperitoneally for 7days and locomotor activity was monitored daily using a 15′′ × 15′′ Plexiglas chamber; after the seventh injection, locomotor activity was threefold higher in mice receiving Cocaine than in mice receiving Saline. Animals were sacrificed by decapitation 24h after the final injection with the exception of mice in the Withdrawal groups, which were kept in the home cage for 8 days after the final Cocaine dose prior to tissue harvest.
Growth protocol Adult male C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME; 2–5months old) were group-housed in the animal facility at the University of Connecticut Health Center on a 12h light/dark cycle (lights, 0700–1900h) and handled in accordance with Institutional Animal Care and Use Committee guidelines. After acclimation for 1 week, animals were handled for 1min/day for 2–3days prior to injections. On each treatment day, animals were allowed to acclimate to the behavior room for 45–60min before beginning injections.
Extracted molecule polyA RNA
Extraction protocol Nucleus accumbens punches were taken from individual mice (at least eight animals/treatment group). Total RNA was prepared using TRIzol. Total RNA used for NAc library preparation consisted of equal amounts of RNA from eight individual mice for each treatment. One Saline, one Cocaine and one 8-day Withdrawal mRNA-Seq library was prepared from each pooled RNA sample according to manufacturer’s specifications (Illumina, San Diego, CA, USA). Briefly, total RNA was treated with DNase I; poly(A)+ RNA purified using Dynal magnetic beads (Invitrogen) was fragmented by partial alkaline hydrolysis (Ambion, Grand Island, CA, USA) and reverse-transcribed using random primers and SuperScript II (Invitrogen). cDNA was size-selected (∼200bp insert) on 2% agarose gels.
Libraries were prepared for sequencing using the Paired-End DNA Sample Prep Kit (Illumina). Nucleus accumbens libraries were sequenced in nine lanes (three technical replicates per sample) on an Illumina GAIIx using a 37-cycle paired-end sequencing protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Sequences and quality scores were extracted from image files using GAPipeline software v1.0 or v1.3.2.
Sequences were aligned to the Mus musculus genome (2007, mm9; NCBI Build 37) using Bowtie v0.12.7 permitting multi-alignment and allowing up to two mismatches. Ambiguous alignments were resolved using the Spliced Paired-end Aligner Perl script (Brooks et al. 2011).
Normalized mRNA expression was calculated as RPKM (reads per kilobase gene model per million mapped reads) (Mortazavi et al. 2008) from aligned sequence reads.
Z-scores were computed from frequency data using the following equation: (x − μ)/ σ; x, sample frequency; μ, mean across all samples; σ, standard deviation across all samples.
Gene expression data (Z-scores) were hierarchically clustered using Gene Cluster v3.0; heat maps were generated using Java Treeview v1.1.6r2.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each replicate and composite files of all RPKM values.
Submission date Jan 10, 2013
Last update date May 15, 2019
Contact name Jodi Eipper-Mains
Organization name University of Connecticut Health Center
Department Genetics & Developmental Biology
Lab Graveley
Street address 263 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030
Country USA
Platform ID GPL11002
Series (1)
GSE43410 Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome.
Reanalyzed by GSE80793
Reanalyzed by GSE80797
SRA SRX216178
BioSample SAMN01885415

Supplementary file Size Download File type/resource
GSM1062208_NAc_saline_rep1.rpkm.txt.gz 246.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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