|
| Status |
Public on Jan 06, 2014 |
| Title |
Control group |
| Sample type |
SRA |
| |
|
| Source name |
Rat hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: control
strain: Wistar
age: 5 months
tissue: Hippocampus
|
| Treatment protocol |
Experimental rats were subjected to status epilepticus (induced by stimulating the lateral nucleus of the right amygdala for 20 min), whereas control rats were subjected to sham stimulation.
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was carried out using the mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, US). The quality and quantity of RNA are assessed on the Agilent Bioanalyzer.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit according to the instructions provided by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample B1
|
| Data processing |
Illumina Hiseq2000 used for basecalling.
The 49nt sequence tags will go through the data cleaning analysis first, which includes getting rid of the low quality tags, 5' adaptor contaminants from the 50nt tags, to get credible clean tags.
The length distribution of the clean tags and common and specific sequences between samples will be summarised.
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome. The parameter is soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample
|
| |
|
| Submission date |
Sep 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhen Sun |
| E-mail(s) |
leleya0602@163.com
|
| Phone |
13863985886
|
| Organization name |
Qingdao Municipal Hospital, Taishan Medical University
|
| Street address |
No.5 Donghai Middle Road, Qingdao
|
| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266071 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE50940 |
MicroRNA profiling of rat hippocampus after status epilepticus induced by amygdala stimulation |
|
| Relations |
| BioSample |
SAMN02358204 |
| SRA |
SRX352181 |
