|
| Status |
Public on Jan 20, 2018 |
| Title |
CUMS-Sal rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Rats exposed to chronic stress and treated with saline
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Hippocampus
age: 6-7 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rat hippocampi were collected, snap-frozen in liquid nitrogen. RNA was extracted using TRIzol kit. A total of 3 µg of RNA was used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Rats exposed to chronic stress and treated with saline
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus norvegicus whole genome (rn6) using TopHat2
Fragments per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell C et al., Nature Biotechnology, 2010.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Jan 19, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Kefeng Li |
| E-mail(s) |
kli@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Dr
|
| City |
San Diego |
| ZIP/Postal code |
92103 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE109445 |
RNA sequencing analysis of gene expression in rat hippocampus exposed to chronic stress and albiforin treatment |
|
| Relations |
| BioSample |
SAMN08380418 |
| SRA |
SRX3586557 |
