|
| Status |
Public on May 24, 2016 |
| Title |
LDM [miRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Landrace
gender: female
age: 210 days old
tissue: longissimus dorsi muscle
|
| Treatment protocol |
When being slaughtered, the pigs were kept off feed but given free access to water for 24 h, and then electrically stunned, exsanguinated, scalded and rinsed. Samples were obtained from the intermediate section of the longissimus dorsi and psoas major immediately after exsanguination, and rapidly frozen in liquid nitrogen for sequencing analysis
|
| Growth protocol |
Three female Landrace pigs, no direct and collateral blood relationship within the last 3 generations, were uesd in this study. All pigs were housed in some environment and fed twice a day with the some diet from weaning (28-day-old) to slaughter (210-day-old). The diets formulas meet the National Research Council (NRC 1998) recommendations for the different growth phase. During experiment preiods, the animals were allowed access to feed and water ad libitum and lived under the same normal conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from adipose tissues using TRIzol (Invitrogen) and further purified with RNeasy columns (Qiagen) according to the manufacturer’s protocol.
About 45 μg of total RNA from the two tissues were used for miRNA transcriptome library preparation and sequencing. In briefly, only about 10–40 nt short RNAs were isolated from polyacrylamide gel electrophoresis (PAGE) was combined with adaptors (Illumina, San Diego, CA, USA) and converted to cDNA by RT-PCR. Then the cDNA was single-end sequencing in 36 bp on the Genome Analyzer GA-2 (Illumina) following the recommended protocol for small RNA sequencing.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The reads were then subjected to a series of additional filters with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 21.0: not sequencing adapters; containing no more than 80% A, C, G, or T; containing no more than two N (undetermined bases); containing not only A and C or G and T, being longer than 14 nt or shorter than 27 nt; not containing 10 repeats of any dimer; not originating from porcine known classes of RNAs (i.e. mRNA in NCBI database; rRNA,tRNA, snRNA and snoRNA in Rfam database)
Then the high-quality reads were mapped to the pig genome (Sscrofa10.2) using NCBI Local BLAST following three steps in order: (1) map the high-quality reads to the precursor miRNAs of pig and 24 other mammals in miRBase 19.0; (2) map the mapped high-quality reads to pig genome (Sscrofa10.2) to obtain their genomic locations and annotations using NCBI Local BLAST; (3) cluster the unmapped sequences in step 1 that mapped to the pig genome as putative novel miRNAs, and predict their hairpin RNA structures from the adjacent 60 nt sequences in either direction from the pig genome using UNAFold
The expression of miRNAs in the two samples was normalized by total mappable reads, and the program IDEG6 was employed to detected DE miRNAs among the two libraries. A unique miRNA is considered to be differentially expressed when it simultaneously obtained p < 0.001 under three statistical tests
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: normalized counts
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Linyuan Shen |
| E-mail(s) |
shenlinyuan0815@163.com
|
| Phone |
+86 15181216032
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
211# Huiming Road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL10945 |
| Series (2) |
| GSE81757 |
Genome-wide DNA methylation and mRNA and the microRNA transcriptome profiling between oxidative and glycolytic skeletal muscles [miRNA-seq] |
| GSE81766 |
Genome-wide DNA methylation and mRNA and the microRNA transcriptome profiling between oxidative and glycolytic skeletal muscles |
|
| Relations |
| BioSample |
SAMN05163631 |
| SRA |
SRX1792978 |
