|
| Status |
Public on Nov 12, 2020 |
| Title |
Sample A6 technical replicate d |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal striatum
|
| Organism |
Rattus norvegicus |
| Characteristics |
genetic background: Sprague-Dawley
age: 8-week-old
treatment: 13 physiological serum injections + 3 cocaine injections
|
| 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 500 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 |
Acute response rat, sample A6 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 2.0-beta5. 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 2.4.0k, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from from Ensembl version 84 was used to compute gene expression. 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: tab-delimited text files include transcripts counting for each Sample
|
| |
|
| Submission date |
Jul 11, 2019 |
| Last update date |
Nov 12, 2020 |
| 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 (1) |
| GSE134154 |
Tolerance to cocaine-induced motor effects in rats: transcriptomic regulations in the dorsal striatum |
|
| Relations |
| BioSample |
SAMN12255674 |
| SRA |
SRX6431517 |
