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| Status |
Public on Jan 01, 2020 |
| Title |
B3-White_skin |
| Sample type |
SRA |
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| Source name |
skin tissue
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| Organism |
Sus scrofa |
| Characteristics |
breed: Bama
development stage: adult
tissue: skin
age: 2 year old
skin color: white
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA (3ug each sample) was isolated with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA (each sample) and the Oligo(dT) magnetic head were used for generating RNA-Seq cDNA libraries , and then, RNA -seq was conducted following the manufacturer's standard procedures.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
domestic pig
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| Data processing |
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3).
Transcripts were assembled by Stringtie version 1.3.3.
Mapped reads were merged by Cuffmerge (part of Cufflinks, version 2.2.1) .
Remove coding gene transcripts by Coffcompare (part of Cufflinks, version 2.2.1) (marked by ‘c’ for partial match or ‘=’ for full match), then transcripts longer than 200bp or more than two exons were kept.
Compared each transcript sequence with Pfam-27 database and trimmed out transcripts with p-value<10-4 by Hmmscan.
Compared with uniref and nr database and trim out transcripts with p-value<10-10 by BLASTX (https://blast.ncbi.nlm.nih.gov/)
Predict and calculate coding protential of the remainly transcripts by CPC
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
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| Submission date |
Jan 23, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
LiRui Zhao |
| E-mail(s) |
779052043@qq.com
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| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
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| Street address |
HuiMing road
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (1) |
| GSE125517 |
Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig |
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| Relations |
| BioSample |
SAMN10793403 |
| SRA |
SRX5283397 |
| 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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