|
| Status |
Public on Mar 11, 2024 |
| Title |
Sample NE2 technical replicate d [2018_508d ] |
| Sample type |
SRA |
| |
|
| Source name |
Nucleus accumbens
|
| Organism |
Rattus norvegicus |
| Characteristics |
genetic background: Sprague-Dawley
age: 8 weeks
phenotype: Non dependent Rat (non CPP-E)
treatment: 4 cocaine injections (1 per day), withdrawal 15 days, 1 cocaine injection
tissue: Nucleus accumbens
|
| Treatment protocol |
Rats received either a challenge dose of cocaine (5 mg/kg i.p; cocaine treated rats), or saline (control group) and their preference was immediately measured in the CPP apparatus for 18 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from bilateral nucleus accumbens and caudate putamen with RNeasy Qiagen mini kit according to the lipid tissue protocol of the manufacturer (Qiagen, Courtaboeuf, France).
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Non dependent rat 2 technical replicate d
|
| Data processing |
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.3. Before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.6.1b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from Ensembl version84. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: *.tsv:Tb-delimited text files include transcripts counting for each Sample.
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
|
| Department |
Genomic Core Facility
|
| Street address |
46 rue Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE169666 |
Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine [CPPE, nCPPE, Saline after cocaine reinstatement] |
| GSE169667 |
Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine |
|
| Relations |
| BioSample |
SAMN18496118 |
| SRA |
SRX10447579 |
