|
| Status |
Public on Jun 01, 2017 |
| Title |
experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Nucleus accumbens tissue from water exposed rats_experiment2
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Brain
tissue compartment: Nucleus accumbens
breed: Wistar
Sex: male
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Lipid tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Transcriptome data from rat nucleus accumbens
|
| Data processing |
Bcl to Fastq conversion was performed using bcl2Fastq v1.8 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for low-quality sequences, then mapped to Rnor_6.0 whole genome using tophat2 v2.0.13 with parameters -p 8 -r 100
Number of reads mapping to each feacher (from SAM file) were calculated using htseq-count v0.5.3p3.
Differential expression analysis was done using DESeq2 package v1.6.2 form R/Bioconductor with the htseq-count result as an input.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The raw counts were generated from the aligned bam files (aligned with Tophat2) using htseq_count version 0.6.0.
|
| |
|
| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Morud |
| E-mail(s) |
julia.morud@neuro.gu.se
|
| Organization name |
University of Gothenburg
|
| Street address |
Beroendemedicin, Box 410
|
| City |
Gothenburg |
| ZIP/Postal code |
405 30 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE73627 |
Genome-wide analysis of nucleus accumbens gene expression after ethanol consumption in rat |
|
| Relations |
| BioSample |
SAMN04001561 |
| SRA |
SRX1160260 |
