|
| Status |
Public on Aug 31, 2022 |
| Title |
LW119 |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi muscle, high intramuscular fat content
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: longissimus dorsi muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the longissimus dorsi muscles of the selected six pigs using TRIzol reagent (Invitrogen). 3 ug of total RNA was used for the construction of sequencing libraries.
A chain-specific library was constructed by removing ribosomal RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
By removing adapter reads, reads containing over 0.2% of poly-N, and low quality paired reads (>50% of bases whose Phred scores were<5%) to filter raw reads.
Clean reads for subsequent analysis were obtained by filtering the raw data, checking the Phred score (Q20 and Q30) and GC content.
The clean data were compared and analyzed by Hisat2 (https://daehwankimlab.github.io/hisat2/) using default parameters
Assembly: Sus scrofa reference genome 11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 30, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Tao Su |
| E-mail(s) |
[email protected]
|
| Organization name |
Shandong Cancer Hospital and Institute
|
| Street address |
440 Jiyan Rd
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250117 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE207279 |
The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content). |
|
| Relations |
| BioSample |
SAMN29441518 |
| SRA |
SRX15951987 |
