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Sample GSM1232772 Query DataSets for GSM1232772
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
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
BioSample SAMN02358204
SRA SRX352181

Supplementary file Size Download File type/resource
GSM1232772_Sample_2.txt.gz 4.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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