One of the many steps in our salmonberry project entails getting our samples sequenced. Sequencing determines the exact order of nucleotides within a certain genetic molecule. We will then analyze those sequences using bioinformatics and relate what we find to salmonberry’s health benefits.
Under the umbrella of “sequencing”, there is a plethora of sequencing options to choose from. In general, there is RNA sequencing and DNA sequencing. For different uses, one option can be more advantageous over the other. Regarding the salmonberry and the work we plan to do, getting insight into the functionality of the active genes themselves is a priority. Consequently, RNA sequencing (RNAseq) is the better option for our project both because of its lower cost and because it will give us more useful information on salmonberry genes than RNA sequencing.
There are various sequencing centers across the country that offer these services, so we needed to contact them to figure out what the best rates would be. We used a procedure from a paper on the blackberry genome as a guide for our rate inquiries.
Duke Center for Genomics and Computational Biology has a online estimator (DUGSIM) where you can figure out the cost of several different sequencing services. However, those prices are for much larger services than what we need.
Instead, centers such as the Northwest Genomics Center at the University of Washington have systems more appropriate for our sample sizes: 100 bp (sample length) reads on an Illumina NovaSeq 6000 S2 flow cell (a type of sequencing machine). For 50 million reads per sample, the cost is $320.
In the bigger scheme of things, we’ll use this estimate to plan our crowdfunding amount accordingly.