E-GEOD-38588 - Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

Status
Released on 16 July 2013, last updated on 2 June 2014
Organism
Sus scrofa
Samples (10)
Array (1)
Protocols (5)
Description
The liver transcriptomes of two female groups (High and Low) with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq [accn: SRA053452, subid: 86092, Bioproject: PRJNA168072]. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L) and 270 (H) lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96), as well as between microarrays and RNA-Seq (r=0.72). A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. According to the score information for the first principal component the animals were ranked in two groups and ten females (5 per group) were assayed with high-density oligonucleotide microarray chips (GeneChip® Porcine) from Affymetrix.
Experiment type
transcription profiling by array 
Contacts
Anna Castelló, Jordi Corominas, Josep M Folch, Miguel Pérez-Enciso, Nuria Mach, Yuliaxis Ramayo-Caldas
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-38588.idf.txt
Sample and data relationshipE-GEOD-38588.sdrf.txt
Raw data (1)E-GEOD-38588.raw.1.zip
Processed data (1)E-GEOD-38588.processed.1.zip
Array designA-AFFY-75.adf.txt
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