|
| Status |
Public on Jan 01, 2020 |
| Title |
Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Skin is the largest organ of body, and one function of skin is protecting underly organs away from ultraviolet (UV) radiation damage. Loss of melanocyte will reduce ability of skin to against UV radiation damage. We found Bama Pig can be an ideal model studying loss of melanocyte. In this study, we performed transcriptome profiling of mRNA and long noncoding RNA in Bama pig white skin (absence of melanocyte) and black skin (existence of melanocyte) to provide dataset for clinical researches. Total of 14,900 mRNAs and 7,566 lncRNAs were expressed in the study. Results of hierarchical cluster analysis and principal component analysis (PCA) demonstrated expression of mRNAs and lncRNAs varied greatly between two color skins. 2,342 mRNA were identified as being differentially expressed, including 1,309 genes that were down-regulated in white skin and 1,033 gene that were up-regulated in white skin (P <0.05; |log2(fold change)| > 1). The genes down-regulated in white skin were associated with melanocyte biology, melanocyte function and keratin, while genes up-regulated in white skin were main associated with metabolism pathway, oxidative phosphorylation and citrate cycle (TCA cycle). In addition, we identified 120 differentially expressed lncRNAs. In those lncRNAs, 4 lncRNAs may function in skin biology (TCONS_00019024 and TCONS_00077733) or metabolic (TCONS_00042201 and TCONS_00060772). Our research provides Bama pig skins datasets and could promote clinical researches utilizing Bama pig as model.
|
| |
|
| Overall design |
Three two-year-old female Bama pigs (without relationship) were used to investgate mechanism of 'two end black'. skin samples (8mm of deepth) of two different colour were collected respectively (white skin in back and black skin in buttock) and separated into two groups. Each collected sample was put into 1.5 ml tube with 1ml Trizol reagent and cut up immediately.Finally, the tubes were placed in liquid nitrogen and stored in -80℃ until required for RNA extraction, sequencing and transcriptome analysis.
|
| |
|
| Contributor(s) |
Zhao L, Hu S, Jin L, Tang Q, Li M |
| Citation(s) |
31905971 |
| |
| Submission date |
Jan 23, 2019 |
| Last update date |
Mar 09, 2020 |
| Contact name |
LiRui Zhao |
| E-mail(s) |
779052043@qq.com
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
HuiMing road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platforms (1) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA516660 |
| SRA |
SRP181648 |
Less...
More...