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| Status |
Public on Sep 01, 2020 |
| Title |
RNA-seq of Sus scrofa: skeletal muscle at D120, replicate1 |
| Sample type |
SRA |
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| Source name |
skeletal muscle
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| Organism |
Sus scrofa |
| Characteristics |
strain: Landrance
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol™ reagent (Invitrogen, CA, USA), followed by rRNA depletion and DNaseI treatment (Qiagen, Hilden, Germany).
For each RNA sample, a paired-end strand-specific library was constructed with an insert size of ~350 bp according to the Illumina Ribo-Zero protocol. The RNA-seq libraries were sequenced on the Illumina HiSeq X Ten platform (Illumina, CA, USA) and 150-bp paired-end reads were generated (Novogene, Beijing, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Covaris S220 software used for basecalling.
After removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data using the Trimmomatic software, the RNA-seq reads were aligned to the porcine reference genome using Hisat2 (v2.0.4) with parameter of --rna-strandness RF, other parameters were set as default.
The expression level of each gene was quantified by calculating fragments per kilobase of exon per million fragments (FPKM) values using StringTie (v1.3.1) in a reference-based approach.
Genome_build: Suscrofa 11.1
Supplementary_files_format_and_content: Landrance_muscle_FPKM.xlsx
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| Submission date |
Aug 28, 2020 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Zhonglin Tang |
| E-mail(s) |
tangzhonglin@caas.cn
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Agricultural Genome Institute at Shenzhen
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| Street address |
No.7, Pengfei road, Dapeng District
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| City |
Shenzhen |
| State/province |
GuangDong |
| ZIP/Postal code |
518100 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (2) |
| GSE157044 |
RNA-seq across 27 developmental stages in Sus scrofa skeletal muscle |
| GSE157045 |
27 developmental stages in Sus scrofa skeletal muscle |
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| Relations |
| BioSample |
SAMN09840147 |
| SRA |
SRX4581399 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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