|
| Status |
Public on Feb 25, 2021 |
| Title |
Ctl 3 |
| Sample type |
SRA |
| |
|
| Source name |
Ctl_primary hippocampus tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
Sex: male
experitment design: Experitment design 1
treatment group: Ctl
treatment: PN 26-28 rats treated with an extra bottle of reverse osmosis-filtered water till PN104
tissue: Primary hippocampus tissue
|
| Treatment protocol |
As shown in the sample 'characteristics: treatment'
|
| Growth protocol |
Juvenile male Sprague Dawley rats (Envigo; arrival post natal day (PN) 26-28; 50-70g) were housed individually in standard conditions with a 12:12 light/dark cycle. All rats had ad libitum access to water and Lab Diet 5001 (PMI Nutrition International, Brentwood, MO; 29.8 % kcal from protein, 13.4% kcal from fat, 56.7% kcal from carbohydrate), with modifications where noted. All experiments were performed in accordance with the approval of the Animal Care and Use Committee at the University of Southern California.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted according to manufacturer’s instructions using RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). Total RNA was checked for degradation in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA)
libraries were prepared from 1 ug of total RNA using a NuGen Universal Plus mRNA-seq Library Prep Kit (Tecan Genomics Inc. Redwood City, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
J1308_S29
|
| Data processing |
Data quality checks were performed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and low quality reads were trimmed with Trim_Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
RNA-seq reads passing quality control were mapped to Rattus novegicus transcriptome (Rnor6) and quantified with Salmon.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab limited files containing raw counts of each sample
|
| |
|
| Submission date |
May 07, 2020 |
| Last update date |
Feb 27, 2021 |
| Contact name |
Yen-Wei Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Los Angeles
|
| Department |
IDP Molecular Toxicology
|
| Street address |
650 Charles E. Young Dr. South 16-035 Center for Health Sciences
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL25029 |
| Series (1) |
| GSE150091 |
The gut microbiome regulates memory function. |
|
| Relations |
| BioSample |
SAMN14851946 |
| SRA |
SRX8296511 |
