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| Status |
Public on Dec 25, 2015 |
| Title |
longissimus dorsi_E90d |
| Sample type |
SRA |
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| Source name |
muscle tissues
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| Organism |
Sus scrofa |
| Characteristics |
gender: female
strain: Jinhua
tissue: muscle
developmental stage: E90 day
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| Extracted molecule |
total RNA |
| Extraction protocol |
The longissimus dorsi muscle tissues from the same area were collected at E90, 0, 30, 180 days and 7 years. Subsequently, the samples were immediately frozen in liquid nitrogen and stored at −80°C until RNA extraction. Total RNAs were isolated from each sample using Trizol (Takara) according to the manufacturer’s protocol.
The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using Illumina Genome Analyzer II according to manufacturer instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
small RNA
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| Data processing |
The reads that passed through a series of additional filters are called “mappable reads”, which are sequences satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 19.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database).
Genome_build: miRBbase 19.0
Supplementary_files_format_and_content: Excel files with read counts
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| Submission date |
Nov 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chaowei Zhou |
| E-mail(s) |
zcwlzq666@163.com
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| Organization name |
Sichuan Agricultural University
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| Street address |
6
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| City |
Sichuan |
| ZIP/Postal code |
625014 |
| Country |
China |
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| Platform ID |
GPL10945 |
| Series (1) |
| GSE75223 |
MicroRNA transcriptome profiles during swine muscle development |
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| Relations |
| BioSample |
SAMN04281010 |
| SRA |
SRX1440075 |
| 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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