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| Status |
Public on Jan 15, 2015 |
| Title |
RNA-Sequencing of lean, intermediate, and obese pigs |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We sequenced mRNA from subcuteneous adipose tissue of 36 pigs (12 Low, 12 Mean and 12 High) to investigate expression profiling of obesity (porcine model). Uploaded RNAseq data on the first 12 samples (from titles 1_SusScrofa to 12_SusScrofa) are LOW obese pigs, the middle 12 samples (from titles 13_SusScrofa to 24_SusScrofa) are MEDIUM obese pigs and the last 12 samples (from titles 24_SusScrofa to 36_SusScrofa) are HIGH obese pigs. These 3 categories based on an aggregate Obesity Index (OI) values and calculated using a multi-trait Estimated Breeding Value (EBV) and Selection Index methods combining nine obesity and obesity-related (OOR) phenotypes into a single value representative of the genetic predisposition to obesity. in Human studies, this is somewhat equivalent to combined multi-trait, weighted Polygenic Risk Scores (PRS) for obesity. That is, they are predicted based on genetic / genomic information and several correlated phenotypes using Mixed Models / BLUP. For more information on Obesity Index, refer to Frontiers in Genetics (2014), Sec. Systems Biology, Vol. 5. https://doi.org/10.3389/fgene.2014.00214
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| |
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| Overall design |
Examination of mRNA levels in different "genetically" categorized obese states in a porcine model for human obesity
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| |
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| Contributor(s) |
Kadarmideen HN, Kogelman LJ |
| Citation(s) |
25270054, 26482556 |
| |
| Submission date |
Sep 09, 2014 |
| Last update date |
Jul 15, 2024 |
| Contact name |
Haja N Kadarmideen |
| E-mail(s) |
hajak@dtu.dk
|
| Organization name |
Technical University of Denmark
|
| Department |
Department of Applied Mathematics and Computer Science
|
| Lab |
Quantitative Genomics, Bioinformatics & Computational Biology (QBC) Group
|
| Street address |
Richard Petersens Plads, Building 324
|
| City |
Kongens Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
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| Platforms (1) |
| GPL19176 |
Illumina HiSeq 2500 (Sus scrofa) |
|
| Samples (36)
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|
| Relations |
| BioProject |
PRJNA260632 |
| SRA |
SRP046752 |
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