|
| Status |
Public on Sep 04, 2022 |
| Title |
Sham _Raphe_Rep5 |
| Sample type |
SRA |
| |
|
| Source name |
Raphe
|
| Organism |
Rattus norvegicus |
| Characteristics |
brain region name: Raphe
treatment: Sham
|
| Treatment protocol |
2 month old Charles River rats were treated with 18mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks
|
| Growth protocol |
Tissue RNA-seq. Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 76 bp read length RNA-seq was carried out on the Illumina HiSeq 2500 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseq
|
| Data processing |
RNA-seq data were aligned to the Rattus norvegicus rn5 genome (Rn5 ENSEMBL) with the STAR aligner. Read counts were concurrently calculated using HTseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Genome_build: Rn5
Supplementary_files_format_and_content: fastq and read count files
|
| |
|
| Submission date |
Jan 24, 2022 |
| Last update date |
Sep 04, 2022 |
| Contact name |
Nirmala Arul Rayan |
| E-mail(s) |
arulrayan@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE194289 |
Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq] |
|
| Relations |
| BioSample |
SAMN25227476 |
| SRA |
SRX13884744 |
