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Sample GSM1915261 Query DataSets for GSM1915261
Status Public on Feb 09, 2017
Title L30-3 (egg-laying)
Sample type SRA
 
Source name Liver
Organism Gallus gallus
Characteristics breed: Lushi
age: 30 weeks
Sex: female
tissue: liver
Extracted molecule total RNA
Extraction protocol All the chickens were raised in cages under the same environment with ad libitum water and food. Healthy individuals were randomly sampled and then slaughtered at juvenile of 20 weeks (20w group) and egg-laying stages of 30 weeks (30w group). The liver tissue was immediately collected, snap-frozen in liquid nitrogen, and stored under -80°C. The small RNA used for sequencing was extracted with mirVana™ miRNA Isolation Kit (Austin TX, US) according to the manufacturer’s instruction. The quality and quantity of the total RNA were assessed by the Agilent 2100
Briefly, 3’ and 5’ RNA adapters were ligated to the total RNA with T4 RNA ligase, successively. Subsequently, the ligated RNAs were subjected to reverse-transcriped PCR to synthesis cDNA, and then the cDNA was amplified by PCR. The amplification products with appropriate length were purified from agarose gel to construct sequence libraries, and then were sequenced with a single-read 1×36 nt multiplex procedure on an Illumina HiSeq 2500 following the manufacturer’s instruction (Illumina).
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
 
Data processing The adaptor sequences and low-quality reads including those unknown bases N, sequences smaller than 18nt and bases quality less than 10 were eliminated by using Fastx (fastx_toolkit-0.0.13.2).
The clean reads from each sample was aligned to the latest Sanger miRBase database 20.0 (http://www.mirbase.org/)
The miRCat tool in sRNA Toolkit software package was used to predict novel miRNA.
Genome_build: Gallus gallus4.0
Supplementary_files_format_and_content: Text files include miRNAs TPM values for each Sample
 
Submission date Oct 21, 2015
Last update date May 15, 2019
Contact name HONG LI
E-mail(s) lihong19871202@163.com
Organization name Henan Agriculture University
Street address 95 Wenhua Road, Jinshui District
City Zheng
ZIP/Postal code 450002
Country China
 
Platform ID GPL13797
Series (1)
GSE74242 miRNA expression profiling in liver of juvenile and egg-laying hens
Relations
BioSample SAMN04201504
SRA SRX1361003

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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