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| Status |
Public on Apr 22, 2024 |
| Title |
HC2_Ribo |
| Sample type |
SRA |
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| Source name |
the longissimus dorsi muscles
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| Organism |
Sus scrofa |
| Characteristics |
tissue: the longissimus dorsi muscles
treatment: calcium supplement
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| Treatment protocol |
At the end of the experiment, the pigs were euthanized through bloodletting. Samples were taken from the selected pigs’ blood, backfat, and longissimus dorsi muscle.
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| Extracted molecule |
other |
| Extraction protocol |
Ribo-seq:In a nutshell, ribosome protected mRNA is obtained through MNase digestion and RNA purification. Briefly, the longissimus dorsi muscle samples were ground in liquid nitrogen and extracted with 800 μL of polysome lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 24 U/mL TurboDNase, 100 μg/mL cycloheximide, 1 mM dithiothreitol (DTT), 1% Triton X-100, and protease inhibitor mixture) for 30 min.
Ribo-seq libraries were prepared according to reference with a minor modification. In total, 5 μg of ribosome-protected mRNA was used to prepare a library with the NEBNext Multiple Small RNA Library Prep Set for Illumina HiSeqX Ten. Briefly, adapters were added to both ends of Ribosome footprints (RFPs), followed by reverse transcription and PCR amplification.
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads containing more than 50% low quality bases, or more than 10% N bases were discarded. The FANSe2 algorithm was used to retain, and map reads between the lengths of 15 and 35 to the reference genome, while the edgeR package’s RPKM (Reads Per Kilobase of Transcript per Million mapped Reads) function was used to normalize the relative abundance between two groups.
Assembly: Sus_scrofa.11.1
Supplementary files format and content: bigWig
Library strategy: Ribo-seq
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| Submission date |
Apr 22, 2024 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Jingsu Yu |
| Organization name |
Guangxi University
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| Department |
College of Animal Science and Technology
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| Street address |
Daxuedong Road, Xixiangtang District
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| City |
Nanning |
| State/province |
Guangxi |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (1) |
| GSE264551 |
Translatomics reveals the role of dietary calcium addition in regulating muscle fat deposition in pigs |
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| Relations |
| BioSample |
SAMN41045351 |
| SRA |
SRX24335698 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8221227_Ribo_HC2.bw |
1.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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