Project description:Identification of differentially expressed genes from RNA-seq data of non-embryogenic and embryogenic ortets. Selected ortets were previously cloned, thereby somatic embryogenesis rates are known for these ortets. Ortets fitting the study criteria were supplied by two agencies, namely L1 and L2. Principal Component Analysis indicated that variance between agencies were higher than the variance between embryogenesis groups within the agency. Therefore, differential analysis was conducted separately for each agency. Differential expression analysis using DESeq2 package suggested the L2 transcriptomes of zero and low embryogenesis groups were more similar compared to the high embryogenesis group. The L1 transcriptomes consisting of zero and low embryogenesis groups similarly showed overlapping clusters. Differential expression analysis was conducted on the L1 samples (low vs. zero embryogenesis) using DESeq2 R package and the identified differentially expressed genes (DEGs) was used for clustering analysis of the L2 samples. The clustering profiles suggested that expression of these DEGs in L2 samples were able to differentiate high embryogenesis from zero-low embryogenesis L2 groups.
Project description:Total proteins were extracted from randomly selected mesocarp fruitlets and subjected to label-free liquid chromatography mass spectrometry.
Mass spectra were acquired using Thermo Xcalibur and deconvoluted with Proteome Discoverer 2.2 to create the mass list. Sequsest search engine was used to match the generated mass list against Elaeis guineensis and Phoenix datylifera protein sequences in NCBI. Standard protein search parameters were applied.
