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Status |
Public on Feb 09, 2017 |
Title |
L20-1 (juvenile) |
Sample type |
SRA |
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Source name |
Liver
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Organism |
Gallus gallus |
Characteristics |
breed: Lushi age: 20 weeks Sex: female tissue: liver
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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).
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Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina Genome Analyzer IIx |
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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
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Submission date |
Oct 21, 2015 |
Last update date |
May 15, 2019 |
Contact name |
HONG LI |
E-mail(s) |
lihong19871202@163.com
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Organization name |
Henan Agriculture University
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Street address |
95 Wenhua Road, Jinshui District
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City |
Zheng |
ZIP/Postal code |
450002 |
Country |
China |
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Platform ID |
GPL13797 |
Series (1) |
GSE74242 |
miRNA expression profiling in liver of juvenile and egg-laying hens |
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Relations |
BioSample |
SAMN04201499 |
SRA |
SRX1360998 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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