|
| Status |
Public on Feb 09, 2017 |
| Title |
TLE group |
| Sample type |
SRA |
| |
|
| Source name |
Rat hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: 3 months
tissue: Hippocampus
|
| Treatment protocol |
TLE rats were subjected to amygdala stimulation (stimulating the lateral nucleus of the right amygdala for 20 min), whereas control rats were subjected to sham stimulation. Total RNA were extracted at 2 months after amygdala 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 A1
|
| 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: hg 19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample
|
| |
|
| Submission date |
Nov 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Teng Jiang |
| E-mail(s) |
jt870918@163.com
|
| Phone |
13851785757
|
| Organization name |
Nanjing Medical University
|
| Department |
Neurology
|
| Street address |
No.140 Hanzhong Road
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE52443 |
Genome-wide microRNA expression profiles of rat hippocampus in a chronic temporal lobe epilepsy model induced by amygdala stimulation |
|
| Relations |
| BioSample |
SAMN02404649 |
| SRA |
SRX378243 |
