|
| Status |
Public on Dec 20, 2010 |
| Title |
2268 LD, small RNA |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi muscle
|
| Organism |
Sus scrofa |
| Characteristics |
strain: F2 female from White Duroc × Erhualian
sib: 2268
tissue: longissimus dorsi muscle
developmental stage: Age of 240 days
|
| Treatment protocol |
All samples were put into the liquid nitrogen within 30 min after slaughtering, and then conserved in -80oC ultra freezer until RNA extraction.
|
| Growth protocol |
All animals were housed in the same environmental conditions and had a good body condition. The room temperatures were uncontrolled with natural lighting. Animals were floor fed three times a day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol (invitrogen) from each sample according to the manufacture’s instructions. Remaining DNA was removed with RNase-free DNase I (New England Biolabs) for 30 min at 37 ℃. The quality of total RNA was assessed by the 2100 Bioanalyzer (Agilent) and agarose gel electrophoresis.Small RNA library preparation was performed according to the illumina alternative v1.5 protocol for small RNA Sequencing. Briefly, small RNA sized at 18-30 nt was purified from total RNA through PAGE gel for each of six samples. 3’ and 5’ Illumina RNA adapters were ligated to the small RNA molecules by T4 RNA ligase. The ligated small RNA was subsequently transcribed into cDNA and amplified for 15 cycles with PCR using primers that anneal to the ends of the adapters. After purified with gel, the amplified cDNA constructs were sequenced according to the Illumina GA platform sequencing protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
expression profile of miRNAs
|
| Data processing |
Sequence reads were obtained and filtered using the Illumina Genome Analyzer Pipeline.
small RNA tags were mapped to genome by SOAP2 (Li et al. 2009) to analyze their expression and distribution on the genome
|
| |
|
| Submission date |
Dec 08, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Lusheng Huang |
| E-mail(s) |
Lushenghuang@hotmail.com
|
| Organization name |
Jiangxi Agricultural University
|
| Lab |
Key Laboratory for Animal Biotechnology of Jiangxi Province
|
| Street address |
No. 1101, Zhimin Avenue
|
| City |
Nanchang |
| State/province |
Jiangxi Province |
| ZIP/Postal code |
330045 |
| Country |
China |
| |
|
| Platform ID |
GPL10945 |
| Series (2) |
| GSE25923 |
A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA) |
| GSE26572 |
A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing |
|
| Relations |
| SRA |
SRX033307 |
| BioSample |
SAMN00149504 |
