|
| Status |
Public on Aug 30, 2018 |
| Title |
LDM rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LDM
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Qinyu Pig
age: 178 days old
tissue: longissimus dorsi muscle (LDM)
|
| Growth protocol |
Qinyu pigs were feeded at growth curve inflection point (maximum matabolism rate) (178 days old)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs are extracted by Trizol (Invitrogen).Only the RNA samples that had RNA Integrity Number (RIN) scores > 8 were used for further sequencing. .
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The clean data were obtained by removing reads containing adapters, reads containing over 10 % of poly(N), and low-quality reads (>50 % of the bases had Phred quality scores ≤ 10) from the raw data.
All the downstream analyses were based on the high quality clean data. Pig reference genome and gene annotation files were downloaded from NCBI database (Sscrofa11.1, NCBI). Paired-end clean reads were aligned to the reference genome using Tophat package, the parameters were set as default.
Next, we filtered the assembled novel transcripts from the different libraries to obtain putative lncRNAs following the steps in the pipeline as follows. First, we excluded transcripts that shorter than 200 nt in length, containing less than 2 exons, and containing less than three reads. Next, the coding potential of the remaining transcripts was calculated using the Coding Potential Calculator (CPC) and Coding-Non-Coding Index (CNCI). A transcript with a CPC value lower than -1 and a CNCI value lower than 0 was taken to be an lncRNA.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: identified lncRNAs and reads count for each Sample
|
| |
|
| Submission date |
Aug 28, 2018 |
| Last update date |
Aug 30, 2018 |
| 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 |
GPL22475 |
| Series (1) |
| GSE119137 |
Comprehensive analysis of lncRNAs and circRNAs reflects the functional specialization in oxidative and glycolytic skeletal muscles |
|
| Relations |
| BioSample |
SAMN09927937 |
| SRA |
SRX4617963 |
