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Sample GSM1267068 Query DataSets for GSM1267068
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
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
BioSample SAMN02404649
SRA SRX378243

Supplementary file Size Download File type/resource
GSM1267068_Sample_A1.txt.gz 4.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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