JU Transcriptome Assembly & Differential Expression Experiment Report

experiment comparing the RNA seq of two treatments. the first for growth of Dunaliella cells in inorganic autotropic medium, the second is the same cells growing in mixture of organic and inorganic mixotropic medium. The RNA seq data are already analyzed. and I have the resulting heat map and gene ontologies and a combined transciptome assembly for the used 6 replicates (3 replicates for each treatment of the 2 treatments). I have no experience to guide with detailed instructions. I needed abstract, introduction, materials and methods, results and discussion for the thesis. it needs no software experience but I think you may need use user friendly bioinformatics websites to help you to find interpretations and detect the pathways that are up or down regulated in response to the different conditions of growth for the cells. I also may need to understand some information that you will  provide me on your written manuscript as it is my first RNA seq experiment.