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| Status |
Public on Jan 12, 2011 |
| Title |
A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA) |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals.
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| Overall design |
Examining the complexity of the pig transcriptome in three organs (liver, abdominal fat, longissimus dorsi muscle) from a female full-sib pair.
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| Contributor(s) |
Huang L, Chen C |
| Citation(s) |
21906321 |
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| Submission date |
Dec 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Lusheng Huang |
| E-mail(s) |
Lushenghuang@hotmail.com
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| Organization name |
Jiangxi Agricultural University
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| Lab |
Key Laboratory for Animal Biotechnology of Jiangxi Province
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| Street address |
No. 1101, Zhimin Avenue
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| City |
Nanchang |
| State/province |
Jiangxi Province |
| ZIP/Postal code |
330045 |
| Country |
China |
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| Platforms (1) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE26572 |
A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing |
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| Relations |
| SRA |
SRP006208 |
| BioProject |
PRJNA142279 |
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