Tweet
Experimental design for RNA-seq in a non-model plant species
Hi all, I'm newbie of the forum and I have no experience in the RNA-seq technology.
My aim is to investigate the expression during flower induction in a non-model plant species subjected to abiotic stress which inhibits this process. I wonder about the accuracy of my experimental design. I supposed two different conditions, each made up of 4 capitula within the same plant (tissue to analyze): 1)control (no stress) and 2)plants exposed to stress. Moreover I considered 3 different sampling times to analyze during flower induction. For each condition and time I considered 3 biological replicas. So that there would be 18 libraries (2_conditions * 3_times * 3_biol_replicas). Furthermore all the plants will be grown in the field. Could this uncontrolled condition increase significantly the variation between biological replicates? Do I have to increase replicates number? My idea is to analyze them with Illumina HiSeq 2000 with flow cell. Considering that it is a non-model species, is this technology suitable with my aims at a reasonable cost (under 10K€)?
My aim is to investigate the expression during flower induction in a non-model plant species subjected to abiotic stress which inhibits this process. I wonder about the accuracy of my experimental design. I supposed two different conditions, each made up of 4 capitula within the same plant (tissue to analyze): 1)control (no stress) and 2)plants exposed to stress. Moreover I considered 3 different sampling times to analyze during flower induction. For each condition and time I considered 3 biological replicas. So that there would be 18 libraries (2_conditions * 3_times * 3_biol_replicas). Furthermore all the plants will be grown in the field. Could this uncontrolled condition increase significantly the variation between biological replicates? Do I have to increase replicates number? My idea is to analyze them with Illumina HiSeq 2000 with flow cell. Considering that it is a non-model species, is this technology suitable with my aims at a reasonable cost (under 10K€)?