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| Status |
Public on Aug 31, 2017 |
| Title |
LargeWhite_Rep2 |
| Sample type |
SRA |
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| Source name |
sketetal muscle
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| Organism |
Sus scrofa |
| Characteristics |
breed: Large White
phenotype: Lean
tissue: longissimus dorsi muscle
age: 2-year
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| Extracted molecule |
total RNA |
| Extraction protocol |
Three unrelated 2-year old adult females for both of LargeWhite and MeiShan pigs were used in this study. Sketetal muscle were rapidly separated from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen, and stored at − 80 °C until RNA extraction.
small RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA-seq
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| Data processing |
Illumina Casava1.7 software used for basecalling. All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 20.0. The reads originated from pocine known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 3 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Sus_scrofa (10.2); miRbase 20.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data
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| Submission date |
Oct 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
long ke ren |
| E-mail(s) |
longkeren@163.com
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| Organization name |
sichuan agriculture university
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| Department |
1 Institute of Animal Genetics & Breeding
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| Lab |
pig
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| Street address |
Huimin road, 211#
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| City |
Wen’jiang,Chengu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL11429 |
| Series (1) |
| GSE88860 |
MicroRNAs Expression Profiles Differ between Primary Myofiber of Lean and Obese Pigs breeds |
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| Relations |
| BioSample |
SAMN05915896 |
| SRA |
SRX2250320 |
| 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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