|
| Status |
Public on Dec 30, 2023 |
| Title |
DLC16012334404_low IMF |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi muscle
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc x Luchuan crossed pigs
tissue: longissimus dorsi muscle
imf content: low
|
| Treatment protocol |
Twenty-five minutes postmortem, samples of the longissimus dorsi muscle at the thoracolumbar junction were taken for meat quality trait measurements and RNA extraction.
|
| Growth protocol |
The experimental population was composed of 265 F1 animals from the crossing of 8 Duroc boars and 112 Luchuan sows, which were fed with the same diets at the same farm. All animals were slaughtered by a standardized procedure at the age of 210 days ± 6 days at the same abattoir.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from longissimus dorsi muscle samples with Trizol reagent according to the product instructions. RNA samples were quantified using NanoDrop-2000 spectrophotometers (Thermo Scientific) and checked for purity and integrity using Agilent 2100 bioanalyzer.
The 150-bp paired-end RNA sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep kit for Illumina® (NEB, USA) according to the manufacturer’s protocols and sequenced on the Illumina Hiseq 4000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Clean reads were obtained from the released raw reads through the following quality control steps: 1) remove reads containing adaptor; 2) remove reads containing more than 5% N; 3) remove low-quality reads
Alignment of RNA-seq data was conducted using Hisat2 V2.0.5 with the genome assembly Sscrofa11.1 (GCA_000003025) as the reference.
The aligned reads for each sample were then assembled into transcripts with StringTie v1.3.3 .
The generated transcripts from different samples were merged using the “merge” function of StringTie and yielded the final annotation file (the merged.gtf file)
The differential expression analysis was conducted with Ballgown.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values and raw fragment counts for each sample
|
| |
|
| Submission date |
Jul 20, 2018 |
| Last update date |
Dec 30, 2023 |
| Contact name |
xuewen xu |
| E-mail(s) |
xuewen_xu@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Shizishan street, No.1
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE117414 |
Muscle transcriptome analysis of Duroc x Luchuan crossed pigs with extreme phenotypes of intramuscular fat content using RNA sequencing |
|
| Relations |
| Reanalyzed by |
GSM3529037 |
| BioSample |
SAMN09694794 |
| SRA |
SRX4410902 |
