|
| Status |
Public on Jun 30, 2022 |
| Title |
SPS2 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampal
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: hippocampus
treatment: single prolonged stress (SPS)
|
| Treatment protocol |
SPS rats were restricted with a plastic container for 2 hours (immobilization), then forced to swim (temperature: 24 ± 1 °C, water depth: 40 cm) for 20 minutes with a 15-minute rest. Finally, the rats were anaesthetized until they lost consciousness, and returned to their own cages. Rats in the control group remained in their home cages with no handling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA from the hippocampi of rats using TRIzol reagent. Ribo-Zero rRNA Removal Kits were used to remove the rRNA from total RNA. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit. Quality and quantity of the libraries were controlled by using the BioAnalyzer 2100 system. We denatured 10 pM libraries as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters, and finally sequenced for 150 cycles on an Illumina HiSeq Sequencer.
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 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format;
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Fang Han |
| E-mail(s) |
fhan@cmu.edu.cn
|
| Organization name |
China Medical University
|
| Street address |
No.77 Puhe Road, Shenyang North New Area
|
| City |
Shenyang |
| State/province |
Liaoning |
| ZIP/Postal code |
110122 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE153081 |
Next Generation Sequencing Facilitates Quantitative Analysis of SPS and Control Rats Model |
|
| Relations |
| BioSample |
SAMN15352240 |
| SRA |
SRX8603451 |
